I got the PGN autosaving working and it feels really good to use. So instead of any annoying dialogs you can just quit the program whenever you like and all your games are present when you reload it!
So next step is the AI... Most of the chess programs I've used tend to use the AI (GNUchess or crafty) to do the movement engine and save games so it will be interesting with glChess (which has its own engine and save games). I think I will get the engine to save itself and put hints in the glChess save file. This way the AI should be happy and should be synchronised with glChess after a load. If I don't lets the AI save itself it would loose all its long term strategy.
Oh and a heads-up for my friends who are reading... Be prepared to get thrown a URL and asked if you can install and run glChess without any instructions. I really need some OS virtualisations to test it properly though as once you have installed libraries etc it's always easier to install the second time.