It seems the options are gtk, gtk2, gtk3, lucid or athena, motif. Of course, there are visual differences and one toolkit may be more to your tastes than others. Apart from that, are there any other differences such as with respect to performance or features? For visual consistency with other applications, I used to compile Emacs with gtk, however, when I just compiled it with lucid, I had the impression that rendering might be faster with lucid than with gtk.
There is at least one documented difference: apparently, there is a bug causing a crash of gtk+ emacs daemon, but not lucid emacs.
If you start emacs as a daemon, you will see the following warning:
Warning: due to a long standing Gtk+ bug http://bugzilla.gnome.org/show_bug.cgi?id=85715 Emacs might crash when run in daemon mode and the X11 connection is unexpectedly lost. Using an Emacs configured with --with-x-toolkit=lucid does not have this problem.
Long-standing is definitely appropriate, this bug was reported back in 2002. But some people are still facing it as of 2014 (link).