I'm mostly familiar with the 2e stuff.
Complete Book of Villains had a lot of good advice for DMs. There's really no hard rules in it, so it can be used just as easily with 4e as it could with 2e. It could be used with 1e or the three little books for that matter.
World Builder's Guidebook. Great for fleshing out a campaign setting. Could still be useful today, and has great backwards compatibility with pre-2e stuff.
The compilations: Encyclopedia Magica and Spell Compendiums. Plenty of extra material any DM will find useful. Downside is that the stuff (in particular the magic items) needs conversions for 3e, and the spells would be even harder to work into 4e.
Thief's Handbook was pretty good too, with the thief guild creation section for DMs, and lot of useful NWPs for rogue characters (some of which got pulled into 3e core).
Other setting specific stuff is good. Faiths and Avatars is ok, haven't used it much though since I don't play in FR, but it still has good ideas for sleshing out homebrew pantheons. The spells aren't bad either, but they were all reprinted in the Priest's Spell Compendium. Planewalker's Handbook is an excellent player guide for Planescape.
Don't have a lot of 3e stuff.
Manual of the Planes was excellent, offered the old classic planar setup, with rules for DMs who wanted to do things differently, and an assortment of interesting optional planes. Also good as a reference for people wanting to update Planescape campaigns to 3e.
Oriental Adventures was also pretty good. Lots of different options for the DM to pick and choose from. The Rokugan focus can be easily ignored, and even then, there's some decent material to be had for the plucking (like the Taint rules.)
