I'm currently running Return to the Temple of Elemental Evil (the PCs are about 3/4 of the way through the Outer Fane), and to be honest I'm getting kind of sick of it. Dungeon-crawling is one thing, but this is getting ridiculous.
My memory might be tainted by nostalgia, but I think a much better way of doing "mega-adventures" would be to do it like in the 2e Dark Sun adventure Dragon's Crown: instead of having one big honkin' mega-dungeon, make it a bunch of smaller adventures that lead into one another. Not all of the part adventures even need to have dungeons - though it shouldn't be totally dungeon-free.
However, making an adventure like Dragon's Crown relies in a large part on the setting, since one of the more enjoyable parts of the adventure was that you had to travel all over the world to accomplish it - not that the region covered in the Dark Sun box set was all that huge, really (roughly the size of Spain, IIRC).
Edit: Checking Dragon's Crown, I see that it has seven major parts, some of which have even smaller sub-adventures, plus a total of 14 vignettes that can be added into the adventure here and there.