My Mac Pro is constantly thinking.

Question

I have a Mac Pro desktop that I use as my media center for our house. Often, it will start "thinking" (that clicking/ticking noise that you usually hear when it's starting an application or adjusting files) and won't stop for a VERY long time (last night it went on for about 5 hours). I have tried shutting down all applications that were open, I have tried looking at the Activity Monitor and have found nothing, and I have checked to make sure that there is no malware, yet the problem still persists. It is currently running OS X Lion with all the latest updates, however, this problem has existed on the machine with every OS version I've installed since Tiger.
Has anyone else had this issue? Found a solution? Aside from the constant noise being annoying, it really slows down my system which is not ideal when using this as a media center.
Here are my machine's details:
Purchased  Late December 2006
Processor  2 x 2 GHz Dual-Core Intel Xeon
Memory  2 GB 667 MHz DDR2 FB-DIMM
Graphics  NVIDIA GeForce 7300 GT 256 MB
Software  Mac OS X Lion 10.7.2 (11C74)
Any help that anyone can provide would be very much appreciated.
Thanks
Tim

Answer 1

you don't have enough memory for one
you should clone the system to a new drive, and have redundant backups
Lion? well 10.7.2 is probably okay. There is now no PowerPC code support
Use to be Disk Warrior was a must to maintain hard drives and directory