The Naval Chronicle (Vol 21) gives some additional information on the rescue fleet (that gives a significantly larger value for the number of transports).
Plymouth, Jan. 23.
Arrived this morning the Barfleur, of 100 guns, Rear-admiral Hood; Tonnant, of 80 guns, Rear-admiral de Courcy; Victory, of 100 guns; Implacable, Resolution, Norge, Elizabeth, and Zealous, of 74 guns each; Amazon, Unicorn and Endymion frigates; Mediator store-ship; and Parthian sloop of war, from Corunna; whence they sailed on Wednesday last, with about 400 sail of transports under convoy: nearly 100 of the latter have arrived here in the course of the day, with troops; the remainder are in the channel, under convoy of four sail of the line, and the greatest part will probably put in here.
The Naval Chronicle for 1809, Vol. XXI. pg. 61
So in addition to the ships mentioned in KillingTime's answer, it would appear that the following ships were also present in the operation at Corunna:
HMS Tonnant was an 80-gun third rate under Captain Richard Hancock and carrying the flag of Rear-Admiral Michael de Courcy (Captured from the French at the battle of the Nile).
The following were 74-gun third rates:
HMS Implacable under Captain George MacKensie (also a former French vessel captured after the battle of Trafalgar).
HMS Resolution under Captain George Burlton.
HMS Norge under Captain Edmund Boger (A former Danish ship captured at Copenhagen in 1807)
HMS Elizabeth under Captain Henry Curzon.
HMS Zealous under Captain Thomas Boys.
The Fifth rate frigates were:
HMS Amazon which was rated as 38-gun.
HMS Unicorn which was rated as 32-gun.
HMS Endymion which was rated as 44-gun (and went onto become famous for the capture of USS President).
The Mediator was originally constructed as an East Indiaman and had been converted initially as a 44-gun warship but only served as a store ship at Corunna (under Commander George Blamey).
The Parthian was a Cherokee class sloop of 10 guns under Commander Richard Harward.
Neither the Amazon nor the Unicorn mention Corunna in their service logs so these may have joined the returning fleet in the Channel.
While it's not mentioned in the quoted passage above, it appears that the Audacious (a sister ship of the Zealous) was also present at Corunna, under the command of Captain Thomas le Marchant Gosselin. This would bring the count of "two-deckers" to seven matching the number given in the earlier answer.
While the bulk of the army was taken on board the transports, the naval warships took their share too:
The Barfleur crammed in 819 soldiers, small groups of officers and men from as many as twenty-three different regiments. Together with the crew of 500 seamen, a remarkable total of 1,371 men were on board. The larger, 110-gun Ville de Paris had a crew of 600 but embarked 743 soldiers, making a total of 1,343, among them General Sir David Baird and his staff, 40 soldiers' wives and 7 children. The boats of the 74-gun Audacious destroyed the beached transports and took off General Hope, his staff and stragglers, taking a total of 308 soldiers to Portsmouth. Among the rescued on this ship were 13 wives and children and 33 French prisoners.
Britain Against Napoleon, R.Knight (Allen Lane, 2013) pg. 204