Can anyone point me in the direction of the codes that were used around the time of Trafalgar? I can find the flag designs easily enough, and the famous message, and Number 16, but is there a (preferably online) list of the other codes?
I fear you may have an uphill struggle.At the time of Nelson,the individual "Siganls officer" usually a Midshipman would have copied the various "orders" and "codes" from the Flagships Main Signal Book inti his own ships Signals Book.Also lots of Admirals would have their "own" codes for signals which would then be disseminated to the various subordinate vessels.A lot of signals would be tailored to the task at hand,and be "made up" on the Flagship.As for a Formal list of Signals there must have been a backbone of standard Signals,such as "Form line of Battle" and "Engage the enemy more closely".The should be found in a Publication called "Sailing and Fighting Instructions".You might like to try the IWM and NAtional Maritime Museum,Greenwich.
Also this book maybe of help.
Kent, Barrie, Captain, Signal! A history of Signalling in the Royal Navy (Clanfield: Hyden House 1993)627.72(42) "19" (A general history of naval communications. Contains handy tables showing 'England Expects', Marryat's code, semaphore, and World War Two and present day naval signal flags.)
Also the RN museum have copies of Sailing and Fighting Regulations 1701,etc that are available for research.