Dunno about comparing the official live versions, but if I was compiling a live version of WDaDU from any source, I'd probably go with:
AFiL - Live in Tokyo video
SS - live from summer 1993 (probably the widely circulating Milwaukee show since I was at it)
YJ - the Old Bridge official bootleg from 1996 (I like Derek's take on the song)
TKH - live from World Tourbulence (I prefer the Another Hand intro to the original but like the extended version compared to LatM)
LFaGA - not many options to pick for this one, so WDaDR
AL - my least favorite WDaDU so I don't have much of an opinion, but probably Score
TOWHtStS - played throughout the ToT, but WDaDR is the best sounding version, so that one
OaMoT - the version on LaB is great, but I'm a sucker for the way they did it on the final leg of their tour in 1993, where they tacked the instrumental half of March of the Tyrant on to the end, so I'd go with a performance from then