How can I get the Alt key to work in an X11 application? I'm using an editor that requires X11 and for the most part it works well. I have many commands that use the Alt key and I like to navigate the menus this way as well, but the Alt key doesn't work through X11. 

I found this article on configuring the Alt key for X11 applications, but it didn't work for me. Any other ideas?
I think you want to check "Enable key equivalents under X11" in the Input tab of the X11 Preferences.