Never mind the language, or anything you need to run a program. These are nice little GUI Linux applications which help you in any language you may be working on, whether it be systems scripts in Perl, a web site using PHP and Javascript, or a little C++ app you happen to be writing.
All of these are available in most Linux and FreeBSD repositories, and many are available on other operating systems such as Microsoft Windows and Apple OS X. Most run using QT, but they all work to be desktop agnostic.
meld, available from [http://meldmerge.org/], is a very good diff tool. It can handle up to 3 versions of a file, or diff entire directories, and even assists you in merging differences together.
Don't want the merging? xxdiff [http://furius.ca/xxdiff/] is a low resource application that diffs 2-3 files or two directories (shallow and recursive).
Pysvn svn-workbench [http://pysvn.tigris.org/project_downloads.html] is a nice GUI subversion manager available on FreeBSD, Windows, Linux and OS X. It gives a consistent look and feel to all your desktops, and allows you to do just about all you want to do on your subversion client.
Let the editor wars begin. Everyone has their own favorite programming editor, but mine is geany (well, joe for the CLI). geany is available from [https://www.geany.org/] if it is not in your repository or you are running Microsoft Windows or Apple OS X (also runs on OpenBSD and NetBSD, in addition to FreeBSD. Comes with a basic set of functionality with the ability to add plugins from the huge repository available from the authors and 3rd party sources, available at [https://plugins.geany.org/]. Can't find what you want? Write your own with their excellent documentation on the API.
mySQL Workbench is available from https://dev.mysql.com/downloads/workbench/, but you should really get it out of your distributions repository if possible since in house they only support “grab the source code”, Windows and RedHat type distributions. You can use it with MariaDB, though some of the functionality is broken. The main reason I use this is to get pretty pictures of what my database looks like so I can include it in the documentation with little effort.
Ok, editor wars are over, now let's start the “x term” wars. I love sakura (theoretically [http://www.pleyades.net/david/sakura.php] but see [http://www.pleyades.net/david/projects/sakura]). While David appears to not be doing as much anymore, there are still plenty of commits going on.
Sakura has tabs (I never use them), window titles, colors, fonts and many, many other options available.
Yes, I know I said tools, but just had to include Strawberry Perl ([http://strawberryperl.com/]). Really good Perl for Windows. Even Larry Wall says he uses it when on Windows.