Mac Pro running extremely slow

Question

I can't seem to diagnose this problem. Let's start with the hardware.
Mac Pro, 4GB, Dual 500GB - Raid 0, 250GB, 300GB and external 500GB.
My internal Raid setup (1TB) was nearly full a few weeks ago and I cleared off half the drive onto the external 500GB. Thinking my problem was a full boot drive... That however didn't fix the problem and I actually believe it seems worse now then it was before doing this.
I ordered an additional 4GB Ram yesterday and it should be here sometime mid-week. This is something I needed anyway and wasn't ordered as a fix for this issue, but if I can't solve it, I figure it should go a long way to cutting down the issue.
I DO NOT want to re-install everything from scratch as it would mean having to setup all my apps again and I really don't want to do that...
Symptoms:
Upon boot after everything is loaded, the machine will grind for a minute or two eventually coming to a halt. Further, launching anything (Safari, WoW (heh), Outlook, etc) will cause massive harddrive noise (no loud noises, just excessive grinding) and eventually come up after what feels like forever.
WoW launches on my first-gen macbook about 3x as fast as my mac pro. (To give some comparison).
Apps running at launch:
Parallels (even turned off, speed is roughly the same)
Outlook
Text Expander
Todos
iStat
Hardware monitors:
CPU is next to nothing, almost always flatlined, even when doing excessive loading, obviously CPU is not the issue here.
Memory reports:
Free: 2.55GB
Wired: 606.07MB
Active: 798.62MB
Inactive: 31.77MB
Used: 1.40GB
VM Size: 75.87GB
Page Ins: 290.32MB
Page Outs: 0 Bytes
Swap Used: 0 Bytes
Any help would be GREATLY appreciated. I just want the machine to run like it did, as it sits, it's almost impossible to be productive here...

Answer 1

Wow, I'm proud of your accomplishments. You seem so eager to list them... I'm a software developer who used to do IT and owned a computer store prior to moving exclusively to software development. I know a thing or two as well. But I prefer solutions than waving monikers around.
Consider the following. I deal with hundreds of thousands of small files while developing software. The primary HD was nearly full before removing the vast majority of said files and moving a large chunk of data to an external drive. It is unlikely that OSX's VM file has been recreated since. This being the case, it is EXTREMELY likely that the VM file is HIGHLY fragmented as evidenced by both the excessive load times (quite audible drive noise denoting loading) and low CPU load. This being the case, my initial reaction was to refresh the VM file, eliminating (or greatly reducing) fragmentation.
I came here because I was hoping someone could help with that, or offer another possible solution. Instead I've been insulted and told to buy new hardware. This is not a solution, it's a band-aid. All my data IS backed up and I have ZERO hardware/software problems. Excessive load time does not require new hardware when hardware was previously not an issue.