Ram is about 1/2 in use, four CPUs are all but idle. I tried "Microsoft Server Performance Advisor" with no luck. No entries in the Event Log for hardware failures, etc.
And yet I can click on the start menu and wait 15 seconds for any new attempt. Launching software takes 30 seconds to respond.
The server has an 8 drive WD RE 250 gig each Dell Perc 6 Sata raid array with Intel gigabit network cards.
Anyone have any software titles that could analyze what is going wrong with this server?
RegMon and probably more likely FileMon would be good starting points. I'd also suggest Performance Monitor for getting ongoing information regarding I/O performance, memory stats and CPU usage. I feel obligated to mention Task Monitor as well, but Process Monitor will give you more information than that. Everything I have mentioned is either built into Windows or free SysInternals tools.
What roles does this machine serve, or what is it's general purpose?
Something random to check is your path environment variable.
I've had on a few machines something similar to what you seem to be describing where launching applications was very slow with no indications of system performance issues and once the application started it ran fine.
The cause was the path variable had a network location in it that was no longer valid and so as windows was checking all the locations in path, when it hit that one it would sit and wait till it timed out.
In a command prompt run "echo %PATH%" and take a look through the paths listed for anything that isn't on a physical drive in the machine.