Great question.
I don't know how I'd order them, but here are my personal nominees as of late:
'92 Chicago "speech from Axl's heart"
The Freddie Mercury Tribute show, Axl is just amazing. A particularly amazing Paradise City, and that ending to Bohemian Rhapsody is a classic too.
The intro and performance of Double-Talkin' Jive Paris '92
'06? U.K. performance of Sailing (arena performance)
fan-made vid of Madagascar from way back in the day, 10 years ago? the fan used the best live overall performance of the tune in my opinion, Boston, Dec. 2, 2002, splicing live segments from '02 in...VMAs included.
another fan-made Madagascar vid with a giant plane flying over what appear to be African natives in a boat, warring African soldiers...this one really tied in the human rights element of the song in my opinion.
piano version of Estranged...no vocals. (sounds crazy because as a whole it's one of the greatest, if not thee greatest, GNR songs ever, but lately I've taken a liking to the straight piano demo version)
Nightrain '06 Rock Am Ring
fan-made This I Love, (I think it was banned as it used a bunch of scenes from the Robin Williams' movie, What Dreams May Come), but damn, the song and the movie are a great freakin' combo.
I'm sure folks here will remind me of others that aren't coming to mind for me at the moment.