First everything is organised by generation, then alphabetically by manufacturer and if need be console name. Then alphabetically by title or series but with members of a series in chronological (release not canon) order. If the console has add-ons (say the megadrive with the 32X and megacd) then the games for them are put in their own section at the end of the main consoles games, sorted alphabetically by title or series...
Sounds OTT I know but I have all the computers I have ever owned (baring x86 PC's of course), and have never traded in or sold a game I didn't think was utter crap.