I'm one of those people who can't leave well enough alone. My station is always changing -- including the computers that help everything run!
I've used Ubuntu Linux in the past, however I don't like the way the user interface is changing... It's too much like a tablet for my taste. Tablets are great, but this is a computer! As such, I have switched over to using Xubuntu which uses the Xfce desktop environment. It's set up a lot like Gnome was in previous Ubuntu releases. Like I've said before, I believe ham radio and open-source software share the same spirit. I whish more ham radio software developers shared this view.
With my increased HF operation since buying my first home, I've needed a more powerful logging program than what YFKlog could provide. I wanted something with a graphical interface, but one that still used MySQL on the backend. CQRLog fit this quite nicely. While it does spin up it's own embedded instance of MySQL, you can configure it to use an instance already installed on your computer, which is what I did. I also wrote a couple of perl scripts to upload my data to my logbook every night.
YFKLog is a console-based contact logging program coded in Perl. It uses a curses front end for a more polished look. I started playing around with this a couple years ago and do like some of its features out of simplicity sake. For one, I like the console-based interface. It means I can leave the program on one machine and use it from another using just SSH. YFKlog also uses a database for a backend, which can be either SQLite or MySQL. Using a database means you can do powerful things with outside applications, and it tends to be easier to backup and restore if you need to. I used to use this almost exclusively until I started using CQRlog. I'd previously been working on adding features to YFKlog (as the original developer has no plans to take YFK further) but found that most of what I was looking for was in CQRlog.
Xastir is an open-source APRS mapping and messaging program. It has the ability to interface with many types of TNC's and use many types of maps. It is very versitle, and it runs on a Mac. If you run an operating system that can't run UI-View (Or you just don't want to, since Xastir can run on Windows), use Xastir.
Xastir can be had at the Xastir homepage. It is also available from the package management on many different Linux distributions including Debian and of course Ubuntu, though these packages are a couple dot releases behind.
Not a ham app, but useful to hams. I discovered Minicom recently thanks to someone on the Xastir mailing list. This program works much like Hyperterminal does on Windows. I needed a program to be able to configure my KISS-based TNC (a TNC-X with XTrack module) using one of my laptops. Minicom allows me to be able to connect to my TNC-X wonderfully and make configuration changes. I installed it via Darwin Ports on my mac, and the good ol' Synaptic on Xubuntu. This program also comes in handy every other time you need a serial console!
For those "bird watchers", this program brings open-source satellite tracking to your linux-running computer. Satellite positions (as predicted by telemetry data) are displayed on a flattened map of the globe. Plug in the coordinates of your station, and GPredict can give you time estimates and alerts to birds flying overhead. With GRig, GPredict can swing your antennas to point right at a satellite as it passes! GPredict and GRig can be found at the ground-station page.
N3FJP's Net Manager
Although still for sale, Net Manager will not be updated. It's a gem of an application, though. I use it any time I run one of the Metro Area ARES nets. It is produced by N3FJP, a well known maker of specialty logging programs for a variety of contests. While this is a Windows application, it runs fine under Wine on the linux side. Net Manager is available from N3FJP's website under the "Other Specialty Logs" page.
The apps listed here, you may or may not find on any of the systems here at K0SKW. Most of them are on here because of their development practices, and not necessarily for any usability issues.
Quite possibly the most popular ham radio-related program for any operating system is UI-View. Rightfully so; it installs wonderfully on Windows systems, is packed with features, and it's free! The creator of UI-View passed away in 2004, but his legacy lives on in the user-base of UI-View. It is available here. Please note that given a choice between UI-View, and Xastir, I'd choose Xaster 6 days out of the week, mainly because of how UI-View handles maps.
Ham Radio Deluxe 5
If there was something as popular as that oh-so-popular APRS program for Windows, it'd be Ham Radio Deluxe. HRD allows rig control functions of popular amateur transcievers. The interface will mimic the functions found on the front panel (and menus) of your transciever giving you easy access to everything. It even allows some remote functionality via the internet. I do use HRD in my station, but mainly so that JT65-HF and JT-Alert know frequency information. I don't currently do any rig-control with HRD.
HRD started life as a free app. The original developer sold HRD's source code to another firm. This firm has improved upon HRD, creating HRD version 6. It's supposed to be much improved than version 5, however it is no longer free. I find that for my uses, 6 isn't worth the upgrade price. More information on HRD can be found at the HRD homepage.