Virtually all phonology is empirical in the sense that it seeks to describe actual linguistic data. If you're looking for people to recommend favorites, there will always be a special place in my heart for John McCarthy's work with autosegmental templates in Arabic. Years ago when I read it, it was the first piece in phonology I read that made my jaw drop.
If you're asking for work that's very explicit about field methods, pickings are disappointingly slim. Your best bet is to look at the first-account grammars. If there's a language family in particular you're interested in, I can probably recommend a few things.
