Ahh, here's a topic near and dear to my heart. I use MediaMonkey to keep track of everything because of it's ridiculous amount of control and tagging options. At the top, I use the "Group" tag to separate out video game music from contemporary stuff. Then I set the genre to the game series/franchise (that way if I just want to listen to, say, Final Fantasy mixes, I just filter the "Final Fantasy" genre). One of the Custom tags is used for specific game within a series (ie- Final Fantasy VI). Album is simply "OverClocked Remix". I've recently been thinking of setting up another custom tag to note the original track (so, like, all my "Terra" remixes can be grouped/filtered), but with nearly 1000 tracks, it'd take a really long time to update them all.
My music folder used to be one giant collection, but since I switched to MediaMonkey, I found it worked better to sort the files into folder by Group, Album Artist, then album or game series.
The one thing about the default tagging from the site that I don't like: separating artists by comma. MediaMonkey supports multiple-artist listing by putting a semicolon between entries. Thus, if I want to pull up a specific artist, all of their collab work comes up along with their solo work. With commas, it creates a new artist entry in the database with all the names rolled together. It's no big deal, but I usually have to spend a bit of time manually updating them when a new album releases.