I think very large dungeons tend to limit player choices. Barring teleport, if your PCs are in a HUGE dungeon, they are pretty much stuck there. If they get bored, leaving to do something else is hardly an option.
I think massive dungeons can work. But I don't think they can be used with the traditional mindset. "Clearing" Undermountain is absurd. Even having to clear half of one, like in RtToEE is frustrating and tedious. They just are not single adventure locales.
Also, Crypts should be considered a separate entity. Tomb of Horrors would be madness on a massive scale.
Two massive dungeon types I think that don't work too well are:
1. Enormous randomly sprawling ones with room after room of monsters, traps, tricks, and treasure. Undermountain I think typifies this. It can be fun, but the PCs really need a motivation to be there. Otherwise, I believe, the sense of accomplishment is significantly lowered.
2. The other kind are narrow, very long dungeons. (like RtToEE) This kind of adventure construction is very prevalent these days. The PCs have 2 maybe 3 choice on where they can go, but ultimately each path leads to a single end. Be it Sunless Citadel, Forge of Fury, or any other "linear" "simplified flowchart" dungeon. These are fun for awhile, but after about 50 rooms, I find the fun factor wears thin.
Massive dungeons I think can work are ones like Mines of Moria. Here the 1000+ room dungeon is built not to be overcome, but simply get to through like in LOTR. Most of it is vacant and maps are kept in case PCs get lost. If they want to explore, they can. Sometimes they may have to take different routes to bypass "occupied areas", but generally the goal is to get out, not explore. In this way truly massive dungeons are more like Wilderness adventures and overland travel. The PCs might get lost, but they should be able to get back with a few well placed clues littered throughout the dungeon. If their goal is to find, say, Moradin's lost hammer, then I would warn PCs before entering without some clue on where it may be hidden inside. (just like hunting for a fairy ring in a massive forest) MERPS Moria can be modified to do this "wilderness" theme fairly well and placed in just about any world. (it's also larger in scale than anything I've ever seen published elsewhere)
While the original ToEE and the more complex Rappan Athuk (RA) are well made, if somewhat smaller dungeons, I think they succeed by having many exits and entrances. RA also includes many smaller climaxes and numerous shortcuts to deeper areas. These go a long way to keeping it viable. Path choices are numerous and interweaving, and players can also complete a portion and then return much later to delve for fun without a loss of continuity.