The whole idea of the $ function and who "owns" that "namespace" has become quite muddy.  When I first learned of the use of $ and found that MS was adopting the same notation, I decided to do it as well.  For at the time, I felt that all frameworks simply used it as a quick way to get the reference to a DOM element.  Soon afterwards I learned that frameworks like prototyle use it for much more.  Apparently, MS learned this as well, and decided to switch to $get.  What I never understood is why they went through all the trouble of creating a nice namespace hierarchy, minimizing chances to have conflicting functions, then decided to scrap the whole idea and make shortened alias' with the $.  In essence, they are saying they "own" the $ namespace.  I have commented back and forth on this issue here.

Unfortunatly, I cannot just yank my $() function since I have to worry about backwards compatibility (at the time MS did it they were in beta so they could).  My $ function should be functioning with prototype last time I checked.

Hope this gives you a little more insight.

I dropped MooTools in my module development shortly after this post because I couldn't get all the functionality to work... Jon's function above uses the Prototype ".Extend" method to access that framework's functionality if it is loaded, so like he said above, Prototype should work.