I recently upgraded to the latest version of FogBugz, which is running on some fancy mono runtime now. The previous version I was running was written in PHP, so I could hack it to my hearts delight. My favorite little mod was keeping fogbugz from top posting email replies, because as we all know top posting is for the newbs. It was a pretty easy hack; just find the code in PHP and swap around some vars.
This modification isn't so easy the in latest version. It's a mess of a custom language and xml files and other interesting things. Honestly I didn't try too hard, because I came up with an easier solution.
I made a bookmarklet that'll root through the reply page, take the contents of the textarea and reformat it to how it's meant to be: fbrewrap.jstalk.
Open that script in up JSTalk, use the Edit ▸ Copy as Bookmarklet, and then add it to your Safari toolbar bookmarks. I've got mine as #2 on the list, so Cmd-2 will invoke it.