So far I've had my computer freeze three times because I opened either Chromium, or Skype over top of a full screen Minecraft window. It has frozen when it was running Unity and when it was running the classic desktop environment. Also I was running a Minecraft server at those times and ended up losing my map due to the last freeze-up.
Ubuntu 11.04 Natty Narwhal Mac mini Kernel: 2.6.38
It sounds like you are running a lot of memory intensive programs concurrently.
If you want to check if your swap partition is large enough, install a program called htop. Then before opening your programs, open a terminal and run htop. Pay attention to the bottom two bars of the top section labeled 'Mem' and 'Swp' as you open your programs.
If you are running out of swap you will see your Mem bar fill up, then your Swp bar will fill all the way up followed by your computer freezing up. In this case you can read about how to increase it in the Ubuntu Documentation
This sounds more like a bug then a question, I'm afraid. I suggest you go hunting for somewhere to share a bug report.
However, a lot of people run games in linux on a separate X server. This means they use two different virtual desktops. If you did this you could switch between a desktop with minecraft on full-screen and another with chromium and skype, etc.
This is a relatively complex task, and isn't the direct answer to your question, but you can check out this tutorial/script:
