Was just watching Alien on BD (good god is that image gorgeous...you'd swear it was a new film almost). And it's always amazed me how amazing the use of miniatures in this film really really sell off that it's real. The framing, timing of movement, etc. It's kind of lost art in a way. Kind of wish they'd do it more often. Peter Jackson seems to really love it. Used wonderfully for the LoTR (and undoubtedly for The Hobbit, one would assume) and King Kong. The stuff filmed in them just...looks real. It's a physical object so scale and texture is given off really well in the image.

Anyway..what films use miniatures in the 2000s? All it got are the Jackson films, The Dark Knight, and Batman Begins. I can't really think of anything else. Just an interesting art form that I appreciate a lot.

It's a lost art to be sure. Alien is amazing in every respect of course. I'd rather watch a film that utilizes miniatures/bigatures than almost any recent CGI laden film.

Unfortunately I can't answer your question.

2 that I have seen recently

Hellboy 2
Mutant Chronicles

KILL BILL VOL. 1 (2003) - when the Bride flies in to Tokyo, the plane flies over the miniature cityscape used by Toho in the Godzilla movies.

Speaking of which, every Godzilla film made in the 2000s uses miniatures. Let's see, the list includes:
GODZILLA 2000 (1999)
GODZILLA X MEGAGUIRUS (2000)
GODZILLA MOTHRA KING GHIDORAH: GIANT MONSTERS ALL OUT ATTACK (2001)
GODZILLA X MECHAGODZILLA (2002)
GODZILLA TOKYO SOS (2003)
GODZILLA FINAL WARS (2004)

+ GAMERA THE BRAVE (2006), which was awful.

http://www.imdb.com/name/nm0227759/

I know Revenge of the Sith used a miniature for the sinkhole on Utapau, it's shown on the DVD special features. I'm sure all the Star Wars used them to some extent in spite of all the talk about CG.

nicely done.

I'll have to see HB2 on BD again, I have it. Somehow that escaped me.

Inception used miniature effects extensively.

The Smurfs

The special features on Hellboy 2 show a lot of the miniature work. The first Hellboy, too, for that matter.

I kind of dig how Tarantino uses miniatures in Kill Bill Vol. 1 and makes it obvious they're miniatures on purpose - yet another of his nods to past cinema he loves so much.

I'd think Scorsese used miniatures in Hugo but I have no idea if he did. Seems like the kind of film and the kind of filmmaker that would see value in it.

Team America: World Police

All of the Star Wars prequels used tons of them. Of course they used a lot of CG & that gets all the hype.

Moon (Sam Rockwell) looks like it's all miniatures.

Tiny Furniture

Team American - hmmm, you think? let's just state the obvious ...

one of the dead movies from 04 had the opening scanning an apocalyptic city.

Are you just making up expressions now?

LOTR trilogy used them extensively. EDIT: I see you mentioned that in the OP now.

Many films still do AFAIK.