I have also an "early 2008" Mac Pro with a lot of HDD interal and external. What really speeded it was to transfer the System (10.8.2) to a 256 GB SSD ( crucial M4) . The speed of booting is spectacular : about 15 sec.
First, back up all data immediately, as your boot drive might be failing.
A common cause of a slow user interface is a large set of image or video files on the Desktop with preview icons. If you have more than a dozen or so such files, move them to another folder.
Another possible cause is iCloud activity, especially Photo Stream synchronization. If applicable, uncheck all boxes in the iCloud preference pane and see whether there's an improvement.
Otherwise take the steps below when you notice the slowdown.
Launch the Activity Monitor 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 Activity Monitor in the icon grid.
Select the CPU tab of the Activity Monitor window.
Select All Processes from the menu in the toolbar, if not already selected.
Click the heading of the % CPU column in the process table to sort the entries by CPU usage. You may have to click it twice to get the highest value at the top. What is it, and what is the process? Also post the values for % User, % System, and % Idle at the bottom of the window.
Select the System Memory tab. What values are shown in the bottom part of the window for Page outs and Swap used?
Next, select the Disk Activity tab. Post the approximate values shown for Reads in/sec and Writes out/sec (notReads in and Writes out.)
If you have more than one user account, you must be logged in as an administrator to carry out this step.
Launch the Console application in the same way you launched Activity Monitor. 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.
Select the 50 or so most recent entries in the log. Copy them (command-C) to the Clipboard. Paste (command-V) into a reply to this message. You're looking for entries at the end of the log, not at the beginning.
When posting a log extract, be selective. Don't post more than is requested.
Please do not indiscriminately dump thousands of lines from the log into this discussion.
Important: Some personal information, such as your name, may appear in the log. Anonymize before posting. That should be easy to do if your extract is not too long.