Programs missing from Programs and Features

Hi,
I wonder if someone can help me.
A few weeks back i accidentally downloaded a program that wasn't from a reliable source, which in turn downloaded a bunch of junk on my computer. It was stupid of me, i'm usually really careful!
I managed to get in and remove most of them, but then all of a sudden all but a few of my programs completely disappeared from Programs and features. Flash Player, Google Chrome, Firefox and a few other programs were the only ones hat remained. The major
programs that were missing from the list are still working fine from what i can see, but i didn't get the chance to remove a few items of adware and they are still active on my computer and being as irritating as an STI (i'd imagine...)
On searching online how to remove these parasites, most of the sites suggest uninstalling from Programs and Features, which i can't do because they aren't on the list! All other suggestions have not worked!
I have tried going into safe mode (with and without networking) and setting up another user profile with admin but the list stays the same. 
I can't remember the last time i backed up (Months ago i presume)
Any suggestions?

You should consider opening a thread here
http://www.bleepingcomputer.com/forums/f/103/am-i-infected-what-do-i-do/
after first reading this
http://www.bleepingcomputer.com/forums/t/41987/before-you-post-about-a-problem/
If/when you receive a clean bill of health and are still having problems, repost here.

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