The default out-of-the-box settings are fine.
Advanced Bus-Level Timing can be either on or off (on is default, and preferred). It does help to specificy whether it's enabled or not, if a movie is submitted.
Do not enable Dynamic Recompiler or any of the debug settings.
Firmware settings are preferred default - if you change them, notify so in the submission description if applicable.
When starting a movie, do not start from SRAM (unless it's explicitly needed, and if so, create a verification movie file for the SRAM data - see the
TASVideos movie rules on this). Any date setting is allowed, as long as it correctly plays back without desyncs on an official release.
Any reasonably recent version of DeSmuME is fine - 0.9.9, 0.9.10 or 0.9.11 are all good. Some recommend 0.9.9 because later versions have save issues, but if you don't mind those then 0.9.11 is fine.
That should cover everything.