I don't make Minecraft brickfilms myself (I've never actually played the game) but I've talked about the possibilities in great depth with Minifigure Maniacs, who did one of his own. While the backgrounds in his were CGI, you can still see from that what I personally think is so great about LEGO Minecraft: its visual simplicity, using 'basic' LEGO bricks. Aside from studs, most round edges are a no-no.

Another big no-no, though, is empty sets. I'm not saying you need to build an expansive LEGO world-map, but the best Minecraft brickfilms I've seen have really managed to use simple bricks and building techniques to create visually interesting frames. Titan Pictures and Forlorn Creature are my best examples. Simple bricks mostly, but great to look at. Titan in particular uses levels a lot; rather than just making a flat green surface, it rises and falls, allowing the characters to interact at different levels (playing around with the symbology of levels is a really useful cinematographic tool).

I guess what I'm trying to say is don't feel like you have to stick to the sets. Get as many bulk green, cream, brown and blue bricks as you can on ebay or Bricklink and be creative. If I had to pick a set that I think would be good for brickfilming though, I'd have to agree with you on the crafting box, or maybe The Farm (which I still haven't picked up, curses).

"Nothing goes down 'less I'm involved. No nuggets. No onion rings. No nothin'. A cheeseburger gets sold in the park, I want in! You got fat while we starved on the streets...now it's my turn!" -Harley Morenstein