I like formats that are a common emulator format. Preferably something that isn't specific to a single program (and especially not a single platform). Here's how I would rank them, generally:
.NSF - best. It's a music only format, many emulators and players are available on many platforms. The validity of its playback can easily be checked from multiple angles, including available hardware players. Other examples in this category include .SID, .SPC, .VGM, .AY, .SNDH... Code formats like NSF or SID tend to be ideal for playback on hardware, but logged formats like VGM are less suited for this, so I would rank them very slightly lower.
.GB - good. Will play in any Game Boy emulator, can be tried in multiple emulators to check its validity, works on multiple platforms. The only downside it it's not a music-only format. Other examples include .TAP.
.DMF - poor. Deflemask is multiplatform, so it at least has this advantage, but no program besides Deflemask will play these files. Emulation accuracy is only as good as the single implementation used by Deflemask, and can't really be checked up unless exported in another format (which are already in the good/best category).
.SHO - poor. It's a music only format, and it has multiple players, but very few. It's not directly emulatable, but the alternative requires an illegal ROM as well as savestates why are nonstandard and emulator specific. Multiple platform support is poor, but the ability to inconveniently check up with emulators is a plus. This format is poor, but there aren't really better alternatives at the moment. (Possibly an SPC export would be a better alternative, but is not available currently.)
.BBSONG - worst. Only plays in one program which only runs on windows. Same problems as .DMF, but compounded by a further lack of portability.
Also, for chip music I am still in favour of having a separate "upload source" option so that we have an appropriate place to put FTM/DMF/BBSONG/etc files.