Best configuration that I know of (because it was me who figured it out for Banjo-tooie faq page):
1964 0.8.5 set up in a very specific way
Download Mupen, take its rsp plugin and rename it to rsp.dll and shove it in the plugins folder. Make sure and turn the RSP on in 0.8.5, you need it just to boot the game up.
Download PJ64 1.6, take jabos video plugin 1.6 and dump it in the 1964 plugin folder.
Download 0.9.9 of 1964 and take schibos audio plugin, put that in the plugins folder of 0.8.5 also.
Of course also set up the plugins.
I usually set the CF to 1 for banjo-tooie, nice and smooth, CF2 works nicely too.
With this config the game was nearly perfect for me, the only noticable glitch was the puzzle pieces in Jiggywiggys temple had funny colors on the edges.