Try using a DB to store all your games on. CB 9 Lite 2009 stores up to 32,000 games and you can create multiple DBs within it - such as one for all the games that chess.com analyzed. BTW their analysis mostly sucks, so I'd start using a free chess program (http://winboard.en.softonic.com/) loaded with great free engines such as Houdini, Firebird, Critter and Stockfish to analyze your games with.
You can still contact the staff directly with your suggestion via Help + Support
http://chessbase.com/download/index.asp DOWNLOAD ChessBase Lite 2009 (free - I have used it and recommend it)
http://chessdb.sourceforge.net/ - I never used this one, but it's also free
I've often times looked at my past games and wondered... which ones did I do a computer analysis on?? With hundreds of games it's hard to keep track of which ones you analized, and which you didn't. I think there should be some sort of quick indication of whether you've processed a computer analysis on the finished games list. That way you can quickly find and review those games.