Entire OS has slowed down and likes to stall

Question

What factors can I look in to to cause the entire operating system to slow down dramatically? I can't recall if there was any single instance that started this behavior but it's been several weeks now.
Some examples;
On a fresh reboot, it takes a couple minutes (120-150 seconds) for the menu bar and dock to load up completely.
When I start Safari, it takes at least 20 seconds to just to allow me to either type in the url bar or to select a bookmark from my book mark bar. Once a website is entered, it can take up to a minute to actually load the web site. Many times this behavior with Safari is not secluded to a fresh reboot or restart of Safari. I've been using the browser for a couple hours now and it took more than 15 seconds to load ANY images on apple.com/support, meaning it was just a white page. Firefox is faster but still stalls at times.
Spotlight is slower than normal. Typing a-d-d to open Address book just wasn't all that snappy. Once Address Book opened, it took more time than usual just to load contacts. It shouldn't take ANY time as I recall. Typing p-h-o-t-o-s-h-o-p used to be very fast and responsive and the first suggestion was in fact photoshop. Now Spotlight occasionally hangs as I'm in the processes of typing and can't "think" past p-h-o-t-o so it thinks I want PhotoBooth.
Mail has also been acting slow. Just issuing CMD+N should take a split second but I have to wait for the OS to consider it before decides to create a new mail.
Generally, programs have just been stalling even more frequently than usual and I spent a portion of the day staring at spinning beach balls. I'm considering 30-60 minutes a portion of the day.
I've looked at some of the obvious things; I've eliminated all start up items in the accounts pref pane, I've freed up as much of the HDD as I can so I now have 12GB left on my 90GB partition. I'm currently running VMWare but I'm certain that it's actually having little to zero impact on the system performance. In fact, WinXP is running far more responsive at the moment as it's being emulated by Fusion. I had Tinker Tool installed but eliminated that and have restarted the os a number of times. Nothing seems to be standing out in Activity Monitor as a memory hog. Top items right now are VMWare, Safari, WindowServer and kernal-task.
Some more background...
This is a 1 gen old 15" MacBook Pro with a 2.2 GHz Core 2 Do and 4GB 667 MHz Ram. It occasionally likes to refuse any keyboard or track pad input but I can plug a mouse in and close programs before I restart. When that happens I need to zap PRam to get back to normal. I've probably done that about a dozen times in the last two weeks. I think that make be related to static discharge as I use the laptop. I had it at the Apple store to get the mother board (are they still "mother boards"?) replaced due to a video output problem and when I got it back the embedded serial number was gone so that causes issues with retaining passwords and such while web browsing. I've been informed on this forum that they can fix that at the shop. I've been having issues with the battery as well but just attribute that to an "old" battery. It's only about a year old but doesn't last more than 45 minutes. More recently, it has just decided to shut off with no warning when the battery indicator on the bottom of the computer shows it still has half a charge.
Thanks for any input

Answer 1

Not bad at all. I ran *sudo chmod -RN "/System/Library/User Template"* and it significantly reduced all the messages I received in disk utility. We went from about 40 to 8. The remaining messages are below.
2009-01-30 20:00:01 -0500: Warning: SUID file "System/Library/Filesystems/AppleShare/afpLoad" has been modified and will not be repaired.
2009-01-30 20:00:01 -0500: Warning: SUID file "usr/bin/setregion" has been modified and will not be repaired.
2009-01-30 20:00:09 -0500: Warning: SUID file "System/Library/PrivateFrameworks/Install.framework/Versions/A/Resources/runner " has been modified and will not be repaired.
2009-01-30 20:00:09 -0500: Warning: SUID file "System/Library/Printers/IOMs/LPRIOM.plugin/Contents/MacOS/LPRIOMHelper" has been modified and will not be repaired.
2009-01-30 20:00:09 -0500: Group differs on "private/etc/cups", should be 0, group is 26.
2009-01-30 20:00:09 -0500: Permissions differ on "private/var/spool/cups/cache/rss", should be drwxr-xr-x , they are drwxrwxr-x .
2009-01-30 20:00:13 -0500: ACL missing on "System/Library/User Template/English.lproj/Documents".
2009-01-30 20:00:13 -0500: ACL missing on "System/Library/User Template/English.lproj/Downloads".