I've been been using subtree in a fork of Git personally but can't (safely) use it at work with everyone else (still use submodules there).
This is going to be a problem for github for reasons I put in my blog a few months back: http://zbowling.github.com/blog/2011/11/25/github/
Because Github has their explicit, top down, a-fork-is-only-a-fork-by-clicking-the-fork-button kind of graph between projects, using subtree won't work easily with their online tools to do pull-requests and see the network graph of forks.
Basically my repo is going to have the histories of 7 different projects combined in one repo and from that single repo I will be pushing back changes to all 7 (and others versions of those 7). Github's pull request feature is going to have trouble with that concept because they make the invalid assumption of a single upstream.
There are work arounds for sure like pushing your changes to a staging repo before finally doing a pull-request upstream but that is cumbersome. I'll probably write a shell script to automate it.