Both of those games seem to work fine for me (Banjo-Kazooie has a minor audio-video sync problem). I use N-Rage's controller plugin, all others are default. I find I get better graphics with glN64 as the video plugin, though.
Step aside, people, the Ocarina Guru is here! I have played and completed this game on both the original system and emulation, so I know what I'm on about. Now, where might you be stuck?