Ideas for causes of iMac Running Slowly

Question

My iMac shows symptoms of spinning beach balls (sometimes rainbow, sometimes blue - does that mean anything?) on a number of applications. In addition the machine will sometimes stop completely for 10 secs or more and then resume whatever it was doing. While this effects a number of application Safari and Dragon Dictate are the big problems.
So far I've looked at the following, although I don't know that my analysis has been exhaustive.
1. Caches etc.
I installed Cocktail and have it run everynight when I log out of the account.
2. Age of the Machine (Its a 2007 iMac)
One developer was kind enough to run some tests for me. He had an identical machine and he ran the same test file. His setup showed no delays. File opening and use of the file was all relatively instantaneous. Mine frequently encounters long delays when opening the same file and using the file.
3. Permissions
This was the first thing I looked at. I did a manual repair and now its being done with Cocktail.
4. Reinstall the OS
I did a reinstall of the OS. There was no difference after the installation.
5. Utilities
I have a few untilities running in my menu bar. These were all removed and the machine was restarted without them. No difference in performance.
Additional Information
1. I ran the activity monitor.
When I get a spinning beachball an application/utility called "ScopedBookmarkAgent" is often consuming 95% of the CPU resources. If the spinning beachball lasts a couple of minutes then this application will be consuming large amounts of CPU resources for most of the time. When the machine stops completely I get the impression that the Activity Monitor stops as well. I cannot find any useful information on "ScopedBookmarkAgent" (I'm not a developer) that would suggest why it might be a problem or more importantly how to fix any problems with it.
2. Disk Drive Space
I have approximatly 100GB free on a 500GB drive. The drive is not the original drive, that was replaced by Apple under Apple Care sometime ago.
3. RAM
I have 4GB of RAM, the maximum possible on this machine.
4. OS
I'm running 10.8.4
I'd appreciate any thoughts on possible causes of my problem and suggestions on how to fix them. In particular with regard to "ScopeBookmarkAgent", since it would appear to be a culprit in the problem.

Answer 1

The next time you 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.