Not having been a Maiden fan back when DT toured with them, I may not have appreciated at the time how epic a pairing that was if I had seen it. But I still wish I had. That would have been right up there in my tops. Metallica/Queensryche, as Barto mentioned, is an outstanding pairing that I never saw as well.
My top would have to be: Dream Theater/Queensryche (with Fates being the warmup act for both). This was really a dream bill, with DT being my favorite band, and Queensryche having a bit of a resurgence at the time and having been my favorite band in the '90s. Plus THE JOINT ENCORES! I saw this show twice in a row, so I got to see every encore song in the rotation, which was REALLY amazing. My only gripe, if any, was that QR headlined all dates west of the Mississippi, so DT was the opener rather than the headliner, which I believe shorted them just a bit on the set time. But still probably my all-time favorite show in terms of headiner/opener combo.
Some others (not ranked):
-Dream Theater/Trivium: I did not know Trivium at the time, but this was an excellent show.
-Def Leppard/Tesla (Hysteria/Mechanical Res tour): Def Lep was my favorite at the time, and Tesla was excellent.
-U2/Pretenders/Bodeans (Joshua Tree tour): I don't remember or care about the Bodeans, but the rest of the bill?
-Motley Crue/Whitesnake/Poison/Jetboy (Girls, Girls, Girls/87/Cat Dragged In/pre-Feel the Shake): This was a festival show, so maybe it doesn't count. WS stole the show, and that's who I was there for. But the others put on a solid show as well.
-Quiet Riot/Whitesnake/Kick Axe (Condition Critical/Slide It In/Vices): This was my first show ever, so it has a soft spot in my heart. All three acts brought it.
There are probably a couple of others I am not remembering at the moment as well.