I recently got frustrated enough by the fact that some games (like SMB2) won't work with controllers plugged into the expansion port of the FC.
So I decided to try to fix that and so far I've done SMB2 and D-Pad Hero 2, but I'm willing to do more if anyone cares enough about it and can tell me what games needs fixing.
I guess this is really only useful for people using flashcarts but it's at least something :)
Super Mario Bros 2 (U) Patch (should work against Super Mario USA as well) (http://fc.viskos.org/files/SMB2_EXP.IPS)
D-Pad Hero 2 Patch (http://fc.viskos.org/files/DPH2_EXP.IPS)
Digger T. Rock and American Gladiators are others that don't work with expansion controllers, I'm sure there's a few more though.