Alright here is the scenario, I was on earlier today around 10am est playing in the servers with a few BK guys, then I left and installed a small flash player update, so I restarted my PC and the dang thing took about 15 minutes just go to my windows loading screen, after that the screen went blank for about 15 more minutes before showing me my login screen where I connect to my desktop. Once I login in, my background shows up, but that is it, no task bar, no icons, just my mouse arrow and the background. I can press ctrl+alt+del and the task manager will come up and says that all the programs that are supposed to be running are running. It has never taken this long to restart my computer ever, so this is very peculiar and new to me.

background on the system:
bought all the parts in january, self assembled. Windows xp sp3, amd triple core processor, 4 gigs ram, asus m3478 (i think) mobo, 8800 gt vid card, 750 w psu

If anyone could help me, it would be greatly appreciated.

Go to a Restore Point to get back to a safety.  

Did you check for viruses?  Very possible.

i had a similar issue with my asus motherboard there is an known issue with the nvidia chipset, i had to get it replaced several times before i got a free upgrade that worked but hopefully if it is this you get it sorted quickly,

btw if it is the same issue i had re-installing windows would take about 48 hours and still didn't finish

Saw this solution mentioned on several different boards concerning blank desktop. Vista and XP:

______________________________________________________________________________
No desktop, because...
c:\windows\explorer.exe would not run

It is visible from the command window, via browse, etc
It cannot be moved, renamed, or executed, by any utility

I found this fix at:

http://www.aurcity.com/compdocs/solutionsarchive.asp

All I did was delete the registry entry:

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Image File Execution.options\explorer.exe

The exact procedure (note, you can do this even though there is no desktop)

1. CTRL-Alt-Del to bring up Task Manager.
2. Click File | New Task(run).
3. Type regedit in the Run box and click OK.
4. Browse to the following registry key:

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Image File Execution.options

5. Under this key there will be subkeys named explorer.exe and iexplorer.exe. Delete the explorer and iexplorer keys entirely. They should not be listed under the Image File Execution.Options key.
6. Close the Registry Editor.
7. Restart the computer.


That was all it took! I did this on a Vista system. The "Windows NT" entry in the registry is correct, even though it is a Vista computer. Note that these instructions were posted in 2005, two years before Vista was released, but they worked for me.

Now I'll be doing a thorough Virus/Spyware/Malware cleanup.

I had that same problem but with different software. A simple thing you can try is  un-plug your psu, turn the psu off, hold down the power button for fifteen seconds.  Plug it back in and try it.  This has helped me with occasional software installs and network problems.  It is a minimal try before exploring other solutions.

ok I never tried anything new, still took a long time, but after about 60-70 mins of a blank desktop everything just appeared and everything was fully functional, hopefully it is a one time thing and the next time it wont do that.

i would recommend going into safe mode and run anti-virus there to see if something got in. to enter safe mode press F8 before windows start up screen. it is a pain but might be worth it to see if that is why your desktop crashed. Was the flash player you installed from Adobe? if not I would also remove it in safe made. There are some viruses that disguise themselves as flash player floating around the internet especially on facebook and other community sites.

IF 24 HOURS PASSED YOU MIGHT GO TO RELIABILITY AND PERFORMANCE MONITOR. ONLY NEED TO TYPE REL IN THE SEARCH. iT SHOULD TELL IF ANY EVENTS HAPPENED THAT CAUSED THIS PROBLEM. THAT WAS GOOD INFO NEMA SPOKE OF. THANKS NEMATODE.
i WOULD TRY TO DO A REPAIR WITH THE OPERATING SYSTEM DISK.
THE SAFE MODE IS GREAT FOR RUNNING THE ANTI-VIRUS SCAN, BUT OFTEN TIMES IT'S NOT THE CULPRIT.

I agree with that but it is a good place to start. keep us up to date on whether or not you find the culprit and I agree with you wesly to use the reliability monitor it has saved my butt a couple of times.

Check the event log to see if you have any warning or errors.  I have a work computer that is starting to show similar (although, not a serious) issues as you are reporting.  In my case the hard drive is failing.