Why can't I use .app bundles symlinked into /Applications as default in the 'open with' dialog?
I don't know why, but I have figured it out that if I make the symlink to the Contents directory, then associations work fine.

That is I do the following in a terminal window, using my personal Applications folder as an example:

% mkdir ~/Applications/Emacs.app
% ln -s /usr/local/Cellar/emacs/23.2/Emacs.app/Contents ~/Applications/Emacs.app


Something about putting the symlink inside the Emacs.app gets the bundle recognized.