I use Openoffice spreadsheet, I generally dislike programs because IMO it's full of useless information, I don't care about bar-codes, description, genre, developer, publisher, how many tonnes of plastic used to make the game, rating, etc. Also, I like seeing the games I DON'T have which most collectors programs only track what you have.
My Spreadsheet for all games has only 5-6 columns. with make shift boxes that I add an x into if I have it.
C (Cartridge) | I (Instructions) | B (Box) | O (Overlay if Applicable) | Title | Rarity
I find it much easier to find a game and edit it, plus I can color code games that I've paid for but haven't received yet, insert comments without adding a new column, and easily add a game variation.
I also use RFGeneration database but it isn't ever 100% accurate since it has many titles/variations missing.