So far...not too many. But if you are an import fanatic, you may want to check this list out!
The fine peeps at the Magic Box have listed the Japanese Game Boy list to which games will have problems on the Game Boy Advance. Most shouldn't worry about it seeing is this list is for Japanese games.
Supposedly the games will still play on GBA, but there will be sound glitches.
-Densha de Go
-Densha de Go 2
-Hamster Paradise 3
-Hamster Paradise 2
-Sakura Taisen GB
-Koro Koro Kirby
-Doreamon - Study Fighter 99 Games
-Game of Go
-World Soccer GB2
-Tokimeki Memorial Pocket: Chapter of Culture
-Tokimeki Memorial Pocket: Chapter of Sports