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.
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I'm very interested in this with respect to performance. But I'm not optimistic. =/ – Malabarba Oct 17 '14 at 08:48
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One difference I noted: with gtk support, Emacs prompts for files (e.g. email attachments) using file selection windows. With lucid, Emacs prompts for the path in the minibuffer. – tmalsburg Oct 17 '14 at 18:32
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I installed 24.4 with lucid and realized I can't get the interface that `list-packages` usually gives. It simply shows the list of packages I can install in minibuffer. – Kaushal Modi Oct 19 '14 at 13:52
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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).

T. Verron
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I remember a discussion last year about this bug. People still run into it. _(Though it's possible those people just ran outdated versions)_. – Malabarba Oct 17 '14 at 08:16
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This finally explains the weird behavior I've had with Emacs and multiple X sessions. (If I close one session, the Emacs server crashes and starts taking up a ton of CPU.) – Tikhon Jelvis Oct 17 '14 at 17:31
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I'm using ```GNU Emacs 25.0.50.1``` on Debian unstable. If I compile it with GTK toolkit I get random crashes when using ```emacs --daemon``` and ```emacsclient```. Only with lucid everything works fine. – Boccaperta-IT Feb 04 '15 at 17:11