Some of mine went poof too. I haven't gone through my actual collection yet, but here are the GC games that I noticed were missing...
Paper Mario: TTYD
Star Fox Adventures
Fire Emblem(still in the DB, re-added it)
Mario Kart(still in the DB, re-added it)
I was told Chibi Robo on GC and Mega Man 3 on the NES went missing from another user's collection as well...
"I feel like I could take on the whole Empire myself."