You might also want to have a look at the installation receipt from X11 in /Library/Receipts/.
DesInstaller is a nice little tool to deal with these (it also removes the associated files).
Also keep in mind that although you can start eagle from the Terminal.app (not xTerm) you need to have X11 started already for this to work!
If you still have problems, you could try installating Eagle from a package distribution (iirc Darwinports has it listed).
Hope this helps!