Personally, I use TextMate on the Mac. There's no Freemarker syntax highlighting, but HTML is good enough. I used to use UltraEdit on the PC. The common "useful" feature between the two is being able to put together projects containing just the files of interest to the particular project (e.g. webscripts, client-side javascript, etc.) and not having to hunt around the local file system all the time.
When developing, we tend to use an exploded (i.e. no .war file) version of the webapp and update the webscripts using "ant incremental-tomcat-exploded"
We've got some in-house scripts to help this process (basically wrapping up the common ant targets using 2- or 3-letter shell scripts).
All version control is done using SVN tools, e.g. SmartSVN which has a good built-in filediff tool when merges and updates aren't automatic.
Does that help at all?
Mike