Are there any specific rules regarding the use of emulators, or is it just similar to OOT in the sense that only Pj1.6/1.7 are allowed, with default settings? (or is it just "anything goes" at this point?)

You can read emulator-specific rules at http://zeldaspeedruns.com/leaderboards/mm/any/rules

These rules really should be added to the rules section here, unless I'm just being blind.