Hulk Surprise (334 convicts), located at Cork
Hulk Essex (400 convicts) located at Dublin
Cork Penitentiary (females) (120 convicts).
The total of 854 prisoners noted in the Return is a little short of Charles Bateson total in The Convict Ships (845), but is close and may not account for those who were rejected by the surgeon as being too ill to survive the voyage.
The Hercules convicts came from counties and cities throughout Ireland including Carlow, Down, Antrim, Armagh, Roscommon, Louth, Fermanagh and Dublin. The Belfast Newsletter reported the method used to convey some of them to the hulk at Dublin.....
On Thursday 13th May 1830 three cart loads of convicts, who were sentenced to transportation at last Assizes, passed through Belfast, escorted by a party of soldiers, on their way from Carrickfergus to Dublin. On turning Linen-Hall street, they gave three hearty cheers, which were as heartily repeated by the populace. 
Crimes committed included rape, burglary, highway robbery, house breaking, stealing pigs and horses, pocket picking, embezzlement and desertion. Some were convicted of committing murder at the Macken Riot at Fermanagh which took place in July 1829. The story of the 'Macken Fight,' written by Michael McManus, YDNA Project.......
The New Reformation of 1827 was a Protestant movement against Catholic emancipation in Ireland and it had sprung up at the end of 1826 in County Cavan. Apart from denying them emancipation many Protestants wanted to convert Catholics and.... 450 Catholics were converted in Cavan where they publicly renounced their faith in various Protestant churches. The movement obviously caused much friction in the communities and one side acted as badly as the other - Protestants tried to force Catholics to conform and Catholics tried to persuade ex-Catholics to return to Catholicism. The New Reformation movement spread to Fermanagh and Lord Enniskillen was one of its great supporters. According to one account, he ordered his Catholic tenants to attend Protestant church services or be evicted from their land. Three families, the Duffys, the Maguires and the MacManus, must have refused because they were evicted and settled in the hilly terrain at Ruscaw. So, at the time of the Macken Riot there was a polarisation of the usual religious and political conflict which had been going on in Ireland for many centuries.
The Freemans Journal tells of the fate of some of the prisoners after the trials -
The Battle of Macken - The Montgomeries and McManus who were sentenced by Judge Jebb to be hanged at Enniskillen on Thursday last and whose lives the Duke of Northumberland has been graciously pleased to spare, by commuting their sentence to transportation for life, were brought up on the outside of the Cavan day coach yesterday and sent off to the hulk at Kingstown. We trust the ferment excited in Fermanagh by the trials of those men, and the unfortunate McManus who was executed last week, will induce his Grace to postpone the trial of the other fifteen Catholics who are in prison for the same crime of which they were found guilty. 
Select here to find the names of the men who were convicted of murder at Fermanagh on 23rd March 1830.
Altogether twenty-eight men were conveyed from Enniskillen jail to the Kingstown hulk - 14 were the Macken rioters; 3 for maliciously throwing a horse down a precipice, 3 for horse and cow stealing; 3 for burglary, 2 for attempt at highway robbery, 2 for cutting down Colonel Bartons plantation, and 1 for stealing wearing apparel etc., from a care taker of Sir Henry Brookes. 
Surgeon William Martin
William Martin kept a Medical Journal from 22 May to 22 November 1830, during which time the ship was employed in a passage from Deptford to Kingston and from there to Sydney in New South Wales......
On 13 June 1830 the Hercules arrived in Kingston harbour. A few days prior to her sailing, some of the convicts on board the Essex hulk, stationed at Kingston, set fire to that vessel in three places, close to the water. The flames were fortunately suppressed, and all on board, being upwards of three hundred prisoners, were transmitted, for better security to the Hercules, which had then but recently arrived in the harbour, to convey some of them to New South Wales. 
The Standard reported the incident on 17 June -
The Essex Hulk stationed in Kingston harbour is on fire and nearly consumed! A number of convicts are on board. The sloop of war Trincolo, and the revenue brig Shamrock, with some transports, have sent all their boats to the assistance of the unfortunate prisoners; and a strong force of horse and foot police from the city has been ordered off to Kingston. The Essex was an American Frigate of 36 guns, and was taken during the late war at Valparaiso, by his Majestys frigate Phoebe, of 36 guns commanded by Captain Hillier.
Two hundred men were embarked on the Hercules. Of these nearly 60 were under 20 years of age; about one half from 20 to 30; and the remainder between that and 70. The city and county of Dublin furnished more than one half of the number including a large proportion of the boys, several of whom, even of the boys, had made serious inroads on their constitutions by their previous irregularities and excesses. 
The guard consisted of a detachment of the 17th regt., who were accompanied by 4 women and 3 children under the Command of Major J.W. Bouverie and Lieutenant C.W. Finch. Select here to find convict ships bringing detachments of the 17th regiment.
By the time the Hercules departed Dublin on 3rd July 1830, the surgeon had time to establish a little order and cleanliness amongst the prisoners...........
Immediately after breakfast, when the weather permitted, they were turned up leaving a sufficient number below to clean the prison though roughly, and then joined their companions as soon as their work was properly done. They were kept up during the day and frequently dined on the deck in fine weather. During the voyage the same system was adhered to, only it was necessary to shelter them as much as practicable, from the sun within the tropics, and from the cold on proceeding to the Southward. We had little serious sickness during the voyage but among men so little accustomed to the use of animal food of any description, the change of diet, on proceeding to sea, naturally produced considerable and very general constipation of the bowels, and on approaching the Tropics many slight cases of fever appeared. On rounding the Cape of Good Hope on the 15th Sept and afterwards proceeding to the Southward, the weather became cold and the thermometer, at one time came down so low as 40 degrees. Catarrhal affections then prevailed, but generally were so slight as to require little or no medical treatment.
The Hercules arrived in Port Jackson on Sunday 31st October or 1st November 1830. One hundred and ninety-nine prisoners arrived, one man by the name of Michael White having died on the passage out. The Hercules brought news of the death of King George the Fourth.
The Captain gave the prisoners an excellent character. They were mustered on board by the Colonial Secretary Alexander Macleay on 4th November 1830 and were to be landed on Monday 15th November 1830.
The convict indents include name, age, education, religion, marital status, family, natie place, trade, offence, when and where tried, sentence, prior convictions, physical description and where assigned to on arrival. There are also occasional notes re pardons, deaths and colonial sentences.
Following are some of the notes included in the indents:
Patrick Byrne from Dundalk - three years added to his original sentence by the Liverpool Bench 12 July 1831 for stealing
William Boyan alias Proctor from Carlow. Sent to Norfolk Island and Bathurst for colonial crimes
John Brien from Cork. Clerk and soldier. Court-martialled for mutiny. Received condition pardon dated 1 March 1848
Patrick Carroll from Wicklow. Sentenced to 12 months in irons 5 November 1835 by the Patrick Plains Bench for absconding
Phillip Cassidy age 21 and Edward Cassidy age 18 from Fermanagh were brothers
Alexander Dennison alias McAlister from Manchester, Pressman. Sentenced to 14 years at Moreton Bay, commuted from death recorded on 28 November 1831 for highway robbery
John Doogan from Fermanagh. Drowned in Lake Macquarie 5 October 1833
Patrick Finn was sent to Norfolk Island
James Glennon from Kildare. Died on 15 June 1836 at Woodlands, Hunter River vide letter by James Arndell
Sylvester Grogan, miller from Leitrim. Died in Newcastle Hospital 15 December 1838
Thomas Higgins. Sent to Norfolk Island
Michael Hughes. Age 15 Sentenced in Maitland 15 Octobeer 1832 to 6 months in irons for stealing and killing a pig. Sentenced in Maitland 5 December 1833 7 days in cells. Sentenced in Maitland 24 August 1835 6 months in irons
Martin Heffernan - Sent to Norfolk Island
James Johnston alias Fox. 2 months on treadmill for absconding from Hyde Park Barracks
Michael Lowe - Died in Port Macquarie Hospital 15 July 1836
Michael Moore - Sent to an iron gang 15 March 1836
Hugh McCartney - Sentenced to 3 years at Norfolk Island
James McManus from Fermanagh. Died at Berrima Stockade 14 June 1835
William Quinlan - Died at Wollombi Hospital 13 August 1832
Robert Somerville - from Dublin. Found murdered at Port Macquarie on 24 August 1835.
Michael Toole - Died at Norfolk Island 1 August 1837
The youngest convicts were James Boyd (14), Francis Byrne (14), John Collin (13), James Connolly (alias Henry Fulham) (14) and John Vaughan (13). Some of these boys were sent to the Carters Barracks on arrival.
1). Names of the men who were convicted of murder at Fermanagh on 23 March 1830....Patrick McManus, Thomas Montgomerie, Patrick Montgomerie, James McManus, Patrick McCaffrey, Michael McConnell, Daniel Murphy, Terence McHugh, John Droogan, James Keenan, Thomas Kerrin (Carron), Brian Rooney, Patrick Rooney.
2). County of Down Assizes - Downpatrick - Tuesday, March 30....William McQuilkin, for stealing a mare, the property of John McGreavy, guilty - sentence of death recorded; William Campbell, for stealing in August last, at Banbridge, a sum of money from the person of Patrick Hillan, guilty - to be transported for seven years. George Murphy for stealing three dozen horn combs, the property of James Lamb, in February last, guilty - transportation for seven years. Thomas Sheeran and Thomas Maguire, for stealing a pair of stockings and two pounds of bacon, the property of James Donnelly, on 31st January, guilty - transportation for seven years - Belfast Newsletter 2 April 1830.
3). On Monday evening David Moore, one of the four persons who escaped out of Cavan gaol, by scaling the walls of the prison about eight months ago was lodged there by a party of police. The unfortunate man had been under rule of transportation for stealing timber from Alexander Saunderson, sq., M.P., from whom, as boatman, he enjoyed a handsome salary and a neat residence. He was apprehended at Roslea in Fermanagh, by one of the police at that station. After his escape from prison, he got off in a merchant vessel for America, and rendered himself so useful on board by assisting in working the ship, that his passage money was returned to him, and he engaged as a sailor. The vessel on her return from Hull, for which place she had been freighted, was wrecked off Cork, and Moore then came to the neighbourhood of Roslea to see his wife, where he was recognised and apprehended He has since been committed to the hulk at at Kingstown to undergo his former sentence. This man is the third of the party retaken. - Freemans Journal 22 January 1830.
4). Return of Convicts of the Hercules assigned between 1st January 1832 and 31st March 1832 (Sydney Gazette 14 June 1832; 28 June 1832; 5 July 1832).....
Thomas Byrne, Silk Weaver assigned to John Cobb at Hunters River
James Gregory, Locksmith assigned to Charles Wilkins in Sydney
James Mahony, Gunsmith assigned to John Larnach at Patrick Plains
Thomas McKenna or Kennon, Mason. Assigned to Robert and Helenus Scott at Hunters River
Michael Quinlon, Cooper assigned to Francis Allman at Maitland
5). Convict Ships bringing detachments of the 17th regiment........
Dunvegan Castle departed Sheerness 30 September 1829 - Lieut. John Grey Katherine Stewart Forbes departed Spithead 14 October 1829 - Major Fairtclough 63rd regt., Mermaid departed Sheerness 5 December 1829 - Lieutenant Isaac Blackburn Forth 1 departed Cork 1 January 1830 - Captain James Oliphant Clunie Nithsdale departed Sheerness 1 January 1830 - Captain Robert G. Moffatt Lady Feversham departed Portsmouth 8 April 1830 - Lieutenant Harvey 29th regt., Marquis of Huntley departed Sheerness 9 April 1830 Lieutenant Watson 20th regt., Adrian departed Portsmouth 27 April 1830 - Ensign Reynolds Lord Melville departed the Downs 6 June 1830 - Lieutenant Robert Graham Hercules departed Dublin 3 July 1830 - Major J.W. Bouverie Royal Admiral departed Portsmouth 5 July 1830 - Captain John Church Burrell departed Plymouth 27 July 1830 - Captain John Alexander Edwards Andromeda departed Cork 28 August 1830 - Captain Charles Forbes York departed Sheerness 4 September 1830 - Lieut-Col. Henry Despard Edward departed Cork 17 October 1830 - Captain Deeds Eliza II departed Cork 10 May 1832 - Lieutenant Hewson 4th regiment
 Freemans Journal 3rd April 1830
 Ancestry.com. UK Royal Navy Medical Journals, 1817-1857. Original data: Medical Journals (ADM 101, 804 bundles and volumes). The National Archives. Kew, Richmond, Surrey.
 Belfast Newsletter 18 May 1830 (4). Belfast Newsletter 4 May 1830
 Bateson, Charles Library of Australian History (1983). The convict ships, 1787-1868 (Australian ed). Library of Australian History, Sydney : pp.348-349, 386