Multi-Game Deck Building Tool
You might be interested in these projects:

Generic Collectible Card Game

OCTGN

MWS

For the first one, last updated end 2009 apparently and it seems there's no yugioh support (to be verified) Lots of addons though and scripting language so that might be doable.

You could also try to dig in that list here:
http://forums.mtgsalvation.com/showthread.php?t=56796

PS: I hate you for reminding me that this game is terribly addicting :)
I'll keep the link above in my favorites but will refrain from installing anything! ;)