I have been doing some heavy testing of the latest build of TempGBA (and the other version angelhp linked to), and I noticed some interesting behaviour.
When I trimmed and re-zip the roms I have, (to save space), I notice with the normal TempGBA build, most games run fine (excluding some like Sonic Advance that don't load at all, though I assume putting an uncompressed, untrimmed rom in there will make it work fine), but when I run them with the build angelhp suggested the framelimit seems to break and all the games run superfast, like it's stuck on fast forward/turbo.
Also, it seems the mode7 monkey intro causes a feeze using normatt's bios also, yet using normal GBA bios doesn't cause this issue and the game loads fine.
If I can fix the weird speedup issue, I'll test my logged list of broken games on the latest tempgba build and list any improvements angelhp's linked build fixes. (GT Advance's heavily corrupted graphics for instance would be an interesting thing to see if it's fixed since it's so noticable)
EDIT: Huh. For some reason the speedup glitch isn't happening anymore now. (might have been a side effect from a certain rom loading) but I can confirm already GT Advance 1+2 works better on it. (Though there seems to be a very minor layering issue on GT Advance 2). Though I tried Hamtaro: Ham Ham Heartbreak and it still freezes at the same point. (Though you DO see a little bit of the screen goes to black effect rather than a straight freeze). It also fixes blades of Thunder's control issue so you can get ingame now. (So there definitely are changes there, but exactly what is still unclear). Lego Knights Kingdom also works ingame now as does Duel Masters - Kaijudo Showdown (used to freeze on name entry screen)
EDIT 2: Yeah, it seems angelhp's list of fixes is about right. (I'll edit this again later listing all the guru meditation error games I found in testing anyway)