I'm not very experienced with Terraclips builds (I only own the Buildings set), but I have some thoughts based on my own experiences.
For buildings, it's easy to slap any old clips together to get the general shape you want. If you want the artwork to match up with what's in your head, though, it gets a little trickier. I built a two-story manor house for players to infiltrate, and I found that I had to be very careful if I wanted the tiles to make sense. You don't want a window in an interior wall, for example. And if the second story exterior is wood, then you don't want the second story floors to be stone. And if you have a double-high wall, it's hard to justify a shelf that's 15 feet off the ground. And so on. For that reason, if you're going to be building more than one or two small houses, I'd recommend getting a second Buildings set.
If you want a lot of stone walls, though (for castles, keeps, wizard's towers, etc), then I'm guessing that you'll want to double-up on the City set. I don't own it, but it looks like it's your best bet for creating above-ground stone structures. (I think that one City set will be enough to build the lighthouse I want, but I'm not sure...)
If I were to buy a second copy of any of the Dungeon sets, I'd definitely go with the Vaults of Ruin. I'm positively drooling over the one-story and two-story support columns. The way I see it, building elaborate 3D structures is the entire reason to go with Terraclips over regular maps or tiles. With more support columns, not only could I build more elaborate 3D dungeons, but I could build that bandit treefort I've always wanted.
(The DungeonRise Essentials set comes with "14 Column Supports", but they're only one-story, and I think they're more props than actual support pieces.)I should mention that if you're just going to be building a moderately sized set piece for a particular session, and then tearing it down again after the PCs leave, then you can probably get away with buying just two boxes of clips. If you're going to build big, though, or if you're going to keep your pieces together for a while, then you'll need a lot more.