In Lion (and previous releases) it was in .MacOSX/environment.plist. After upgrading to 10.8, the file is still there, but the variables aren’t taking.
I’ve also tried adding them to /etc/launchd.conf and they’ll show up in Terminal, but not GUI applications (like my IDE).
/etc/launchd.conf? – nohillside Jul 25 '12 at 17:16