The easiest way to edit the list of startup items (which includes items set to auto-run in the registry) is to use msconfig.

Also, don't forget that booting up into a linux live CD and running a virus scan from there can help remove pesky viruses that protect themselves from Windows

Just a though from past experiences...

Hmm, it seems that Microsoft security had found a possible virus, but I must wait the end of the scan... strange..

Also, speed is being very sporadic, I am really going to get flustered if the scan does not finish by 10..
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Having been the guy who gets called by everyone in the area when their computer is "running slow" or "got a virus i think" Ill tell you what you need to do. Download Hiren's BootCD and go under MiniXP and run Malwarebytes Anti-Malware on YOUR C drive (not the RAM drive it creates) then reboot into Mini-XP one more time and run Combo-fix and Hijackthis, when you run hijackthis, mail me the log at cmatheson1@gmail.com and Ill help you further.

Dalton knows his sh!t. Most of those are tools I've used and have saved my computer many times.

The #1 thing to do is to boot your computer into safe mode. (with the F8 key), login as Administrator (the real one!), and run an updated version of ClamWin.
#2 If nothing pops up as a threat, next I would recommend running a registry cleaner. Of course, the ideal situation would be to have a backed-up .reg file you just restore, but that usually ISN'T the case.
#3 If that doesn't work, use a Live CD Linux distro like Knoppix or Puppy to diagnose and destroy the little boogers.
#4 If all else fails, you can use the system restore partition, which automatically deletes and re-installs all system files, leaving all of your data intact. You WILL lose lots of settings and stuff following that route.
#5 When that fails, all you have left to do is to format the hard-disk, and re-install from the beginning. (Or spend 100 bucks on a geek squad guy to do all this process for you... your choice.)

1. Safe mode has the same problems, it is still really slow in safe mode
2. Tried a reg cleaner. I do have a backup actually, I will try that
3. That will be another last resort
4. Last Resort
5. AAANNDDD Last resort!
6. Dalton, I shall try that after I finish another scan/defragment/reg restore

EDIT: Ok, this is really pissing me off, when any scanner is running, my compputer will be faster all of a sudden. WTF? Right after this last scan I will try Dalton's idea

EDIT2: Freaking wonderful, HL.exe is back

I'm about to ban you for that comment. Don't ever ever EVER use Geek Squad or equivalents; they're n00bs who will just as soon give you a totally wrong diagnoses, lose or erase your hard drive, or break things. Don't ever. Just don't.

Once a virus strikes, you may as well reformat. Viruses can embed themselves, leave behind dormant copies, and resurrect those copies if you attempt to remove them. It's a zombie strategy. Once one instance is taken out, the others awaken in its place. Viruses also have a tendency to corrupt and damage whatever they can before being removed. Even if you do clean out your system, you usually won't undo the damage.

I work on computers from my home. I go through these problems all the time. It's honestly easier to just reformat and get it over with. I keep trying to tell people this, but they seem to prefer to learn the hard way. They jump through all these hoops to find individual solutions for a paper trail of problems caused by a virus infection, and end up doing way more work than if they had just decided to reformat and get it over with.

Well, Zera, i would beg to differ. You can very easily completely remove a virus infection and reoptimize the computer back to its original speeds and 99% of the time in my experience recover corruptions if you know where to find the right tools.

Don't get me started. I went to Best Buy once to replace my Mom's harddrive, and they didn't know the difference between EIDE and ESATA. They ended up selling me the wrong goddamn harddrive before swapping it for the correct one. Now the tech guy at Staples on the other hand, he really knew his sh!t, right down to the history of the manufacturers. It might have been a fluke, but might be worth just talking to one.

Well, I booted Ubuntu with a Flash Drive... errm.. now what do I do?

Geek Squad--

I think this is accurate. Maybe they take classes or something. They knew everything I had questions about the last time I visited.

Now you install Ubuntu! I kid, now you delete any files from your Windows partition that you need to.

woot, that ought to be fun ><

I take back the Geek Squad joke because it offended you guys. Geek Squad is for dummies.

@qazz
I wouldn't necessarily choose Ubuntu... I would use a LiveCD with Knoppix or Puppy because they seem to have the better more powerful tools available. Ubuntu is meant as a replacement for Windows or Mac. It has LOTS of cool features, but is pretty heavyweight for what you need. But, you could probably get what's needed to be done accomplished. I wish you luck though! Remember the system restore! When Linux fails, that's all you have left before formatting and enduring severe data loss. Don't listen to the people who say formatting is the first step. It's always the very last one.

Puppy Linux has come in handy for me loads of times. One great advantage is it can be run entirely from RAM, requiring no hard disk space, so you can freely manipulate all your drives however you need to to recover data.

Well, I reformatted, and everything is lookin fine

I cannot help but wonder what the problem was I think it was a program my friend gave me :/

You didn't try just deleting the rogue files when you were running live Linux? Anyway, glad to hear that things are back to normal. Why did you take a program from your friend? I would never do something like that.

*cough* Freebuild *cough*