Virus!!

First unplug your computer from the Internet.
Get Malwarebytes on a USB key or CD from a clean computer.
Don't use one with any valuable data on it.
Then try again.

done that it still does not want to run

Your best option is to download and create a boot up antivirus rescue disk from one of the well known antivirus vendors (e.g., Bitdefender, Trend Micro, Avira, etc.).

Boot up and scan from the CD/DVD/USB rescue disk.

To aadih's comment, I recommend the AVG rescue CD. It is free and has several other tools that might help you out. I've included a link to the download below!

http://www.avg.com/us-en/avg-rescue-cd

Have you tried booting into safe mode and installing and running MWB? While this is not the recommended way to run MWB, many times it will kill off enough of the infection that you can then boot into normal mode and finish the job.  You might also try logging in as another user account; sometimes infections are limited to that account - although that's not usually the way it works.

If you can get mWB to run in safe mode and then can get back into normal mode OK, you might try doing a system restore to a save restore before you got the infection.

There is also an offline version of Windows defender which will boot form a USB key.

And do think about if your data is backed up.
If it is not perhaps you should install a parallel Windows just to backup your data before trying to fix the computer.
If the virus is bad you should rebuild the computer anyway,

Not sure what virus you have, but try the instructions here on running MBAM chameleon.  I have found these very effective.

Ok tried running Kaspersky Boot disk which did detect certain things and I deleted them but still when booting into windows trying to open any .exe files comes up with a dialogue box asking which program I want to open it with.

I have tried the above suggestion also regarding chameleon

John

What is your OS?

Solution here for XP:  < http://www.dougknox.com/xp/fileassoc/xp_exe_fix.zip >

For other OSs: < http://support.microsoft.com/kb/2688326 >