Say, you want spotlight to find MacVim. Doing

$ brew linkapps macvim

creates a symlink in /Applications. But Spotlight seems to ignore it. Instead, remove the symlink

$ rm /Applications/MacVim.app

and do

$ osascript -e 'tell application "Finder" to make alias file to POSIX file "/usr/local/opt/macvim/MacVim.app" at POSIX file "/Applications"'