I organize mine by system as well, then put them in order alphabetically. However, if there are multiple games in a series on a system but their order is messed up by their title, I'll put those into whatever order I feel is best, to keep them all together. For example, my Resident Evil games on PS2 are organized by their chronological placement in the series timeline: RE:Outbreak 1, RE: Outbreak 2, RE:CVX, RE: Dead Aim, RE4.