This site is good: http://cgfm2.emuviews.com/temp/mvstech.txt (it's credited at the top of the mame source)
This site is ok too: http://arcadedev.emuvibes.com/ (read the neogeo spex doc)
Although I've found mame to be more useful than either of these. You can also look at other emulators like gngeo and final burn alpha. Interestingly, I've found the psp neogeo/cpsX emulator to be very easy to read. Once you read the above docs, the emulator source code will probly make more sense (it did for me).
> Not that this will answer your question or anything, but I am interested in
> knowing where you got the documentation necessary for building a Neo Geo
> emulator. I am looking for references besides the traditional "Go look at the
> MAME source you n00b".