It would be nice if we could build the GNU utilities with it. I tried building some of the basic utilities the other day, and there were configure scripts that basically did "If the compiler name doesn't start with gcc then do lots of stupid stuff" which meant it built if I symlinked "gcc-foo" to clang and built with that, but failed if I set CC to clang.
One gripe I have with LLVM/Clang is that it lacks the ability to use linker scripts.
I'm writing a little OS to learn how it all works, and wanted to develop on my native Mac OS instead of an Ubuntu VM, yet Apple have symlinked 'ld' to the llvm linker, which doesn't take linker scripts like gcc's ld does.
The linker included with OS X is known as ld64 (to distinguish it from an older linker). The source code is available from http://opensource.apple.com/source/ld64/ld64-133.3/, but it is not a part of the LLVM project and only uses LLVM for LTO support.
You can produce standalone binaries with it (adding sections and modifying their attributes with command-line arguments), but it doesn't support linker scripts.
You could always use the GNU ld (or gold) with the LLVM output. Binutils is a trivially easy compile on Linux, though I'm not as certain about Darwin.
Editted to add: if you're building your OS with someone else's prepackaged toolchain, you're in for a bunch of hurt. The toolchain is, broadly, part of the OS. Writing a handful of custom linker scripts isn't the only spot where you'll need to hack at this stuff.