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I have had my desktop that has ran Ubuntu over a few years, on my most recent reinstall, periodically (saying once every 10 minutes or so) my system will just freeze. Mouse won't move, keyboard doesn't respond, Flash video is paused (the audio usually continues though). How do I go about handling this?

The only changes since my last install: I had a new graphics card (ATI Radeon 5450 1GB, a huge upgrade from my Radeon 3450 256 MB), and upgraded Ubuntu from 10.10 to 11.04. This in no way should be it hanging due to hardware constraints, the graphics card is sufficient for 3 monitors (through eyefinity), I only use about 3 of 6 GB of ram at a time, and processing stays under 25% (I have a little applet, I can watch it all the time).

How do I start debugging this and any ideas on a particular problem?

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The first step to debugging is going to be checking your system logs. To do this your going to want to open a terminal and change directories to /var/log, to do this type:

cd /var/log

in the terminal.

Then with the text editor of your choice view the kernel ring buffer message. I'll use gedit for this example.

gedit dmesg

Another helpful log will be the messages log. This displays information about applications and system processes. To view this run:

gedit messages

And if you don't find anything that stands out in those two, check the systems log by running

gedit syslog

When your system "hangs" make note of the time, and then when your looking through the logs you can go to that time in the log and look for inconsistencies. If you see anything that stands out you can edit your question and copy/paste in that part of the log.

For more information on the various log files and what they do: https://help.ubuntu.com/community/LinuxLogFiles

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