I've found a game that both GameYob v0.3-104 and Lameboy v0.12 have a lot of trouble with, Moorhuhn 2.
Moorhuhn 2 is a port of a PC title that features a lot of pre-rendered 3D visuals, the GBC version is much the same.
Actual gameplay seems to run fine, maybe the sprite flickering is an issue I'm not sure, but more pressing is the trouble emulating the large pre-rendered FMV stuff.
There are a number of large full-screen graphics that display improperly, like a huhn flying across the screen before the title screen, the title screen itself, the Similis logo, and the credits animation which has photos of developers displayed on 3D computer monitors.
Just try it and you'll see something's up.