I use the save avi functionality of mupen. I usually save a 640x480 x264 file at constant quant 10 (0 is lossless, 51 is shittiest quality). that yielded about a 1GB file for the 11 minutes of video in this case. It recorded as about 10 frames per second (that's 1/6th realtime). then I reencode that (megui is good) to a smaller resolution, and use lame.exe to turn the .wav into .mp3, and then I use mkvmerge to make the encoded video and sound into one .mkv. Not really the best way of doing it, but the files look good, and apart from the wait, and pushing a few buttons waiting, pushing more buttons, and then waiting more, it's not difficult once you've done it once.
I'm sure there are threads detailing other ways, but for n64 recording on windows, the each option is as crappy as the next (mupen HAS to be on top for the entire time you record since it uses the screen data over the mupen rectangle), that's what makes n64 recording so much more annoying than other emulators.
anyway, the vid is from the end of TTC to the end of CC. also part03v2 is still an outdated ttc play. I'll make a video of the entire run so far when sami finishes BGS.
http://bkdj.net/index.php?dir=tas/bk/
filename: banjo_kazooie-wiptas-sami_part04.mkv