Why is my computer "stuttering" while trying to process tasks it's more than capable of handling? (iMovie editing, audio processing, general usage, etc)

Question

I'm really at a loss here.
I recently "upgraded" to a 2008 Mac Pro with 12GB RAM, 2 x 2.8 GHz Quad core processors, 1.5GB VRAM, etc etc. A much better computer than my late 2007 Macbook Pro with a 2.4 GHz Dualcore, 4GB RAM, and 256 MB VRAM.
Despite this massive technical improvement, basic operations still stutter and spurt fairly often. I've checked for Spyware/Viruses/Malware, I've dusted the inside of the tower, I've got plenty of hard drive space left over, and Activity Monitor always has at least 6GB RAM and 75% of the CPU "power" remaining. By all counts, the computer is having no issues at all handling anything I throw at it, and yet... it constantly will freeze for a moment or two, just like my old Macbook Pro used to while it had to load previews of clips in iMovie, load up effects in a music editor, etc etc. It even does this if I full-screen a Youtube video without waiting for it to load fully, or open one program before another one has fully loaded up.
What gives? Why can't I do basic operations without it stuttering a couple of times a minute? The computer is more than capable.

Answer 1

When you next have the problem, note the exact time: hour, minute, second.
If you have more than one user account, these instructions must be carried out as an administrator.
Launch the Console application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Console in the icon grid.
Make sure the title of the Console window is All Messages. If it isn't, select All Messages from the SYSTEM LOG QUERIES menu on the left. If you don't see that menu, select
View ▹ Show Log List
from the menu bar.
Scroll back in the log to the time you noted above. Select any messages timestamped from then until the end of the episode, or until they start to repeat. Copy them to the Clipboard (command-C). Paste into a reply to this message (command-V).
When posting a log extract, be selective. In most cases, a few dozen lines are more than enough.
Please do not indiscriminately dump thousands of lines from the log into this discussion.
Important: Some private information, such as your name, may appear in the log. Anonymize before posting.