I know where you're coming from, Ven, but it's hard for me to preach consistency when I'm not consistent myself. :)
I've been using "Marvel 616" as the character's universe for a few mainstream Marvel characters, primarily where there might be some confusion because of a character with the same name from either a different reality or a different publisher.
Having said that, I've also chucked "Marvel 616" into a few mainstream characters on a whim, even if they didn't have counterparts in other realities.
For realities outside of 616, I've been using "Marvel Earth-XXX" (where "XXX" is the number designated to that universe).
What do others think?