They're sort of a combination.
A .MOD file has the information on how to play the music (like a MIDI) and has the sampled instruments (WAVs) within it. They're made using "tracking" software (NoiseTracker, ScreamTracker, ProTracker, etc.)
I've ripped a number of Amiga mods in my day. *pats his Amiga 4000*
A good place to get mods is http://www.back2roots.org in the Music section.
As for my Top 10... well, I'll have to think on that for a bit. I'll get back to you on that. :)
*dashes off to get mikmod for his GP32...*
Peace...