On recent OS X versions (Lion at the very least), the problem isn't that /Library and ~/Library aren't indexed by default; they are.
Trouble is that if I search for a file named, say "com.apple.RemoteDesktop.plist", Finder appears to run a query akin to
which returns three results, one each in subdirectories of /System/Library, /Library, and ~/Library.
There's an option in the "full" Spotlight search window that lets you control this for any given search, under "Other..." in the drop-down you get when you click "+" to add criteria. It's called, logically enough, "System files".
Incidentally, the mdfind command line tool doesn't have this behavior by default.
If you want a nice GUI, try Tembo (http://www.houdah.com/tembo).
Tembo is a Spotlight front-end. Incidentally it searches all indexed locations, including Library folders.
There's an option in the "full" Spotlight search window that lets you control this for any given search, under "Other..." in the drop-down you get when you click "+" to add criteria. It's called, logically enough, "System files".
Incidentally, the mdfind command line tool doesn't have this behavior by default.