MacOS – Homebrew doctor warning: you have unlinked kegs in your Cellar

Until all the kinks get worked out, you'll want to track 10.7 and Xcode 4.x issues at https://github.com/mxcl/homebrew/issues

In this case, be sure you actively manage your $PATH variable to keep your preferred versions of redundant apps first in the expansion.

Always hard coding full paths is tedious, but lack of it causes these bumps when new binaries show up in your path unexpectedly.

Homebrew developer here: everything should be under /usr/local. Anything not under there would have required manual intervention by you to be put somewhere else (most likely your home directory). Worst case you just read the caveats for the packages that don't appear to work correctly any more.