So I downloaded Frostwire probably about two years ago. It randomly froze and shut down on me, and wouldn't work, so I uninstalled it, and completely deleted it from my computer. I was then in search for a new music source, and found Limewire, which was said to be better than Frostwire. In my opinion, it's really not, only for the fact that it slowed my computer down to the max once I downloaded it. Anyway, I uninstalled Limewire from my computer at that point, but now I'm getting this pop-up every time I turn on my computer. Once I X out of it, it pops right back up about three seconds later. At the top, it says, "One or more necessary files appears to be invalid. This is generally caused by a corrupted installation. Please try downloading and installing Limewire again...." and then it goes on to give a code-source. So, if I download it again, will this message go away? If not, how do I get it to go away? It's really annoying!

How did you uninstall LW? Uninstalling via Add/Remove Programs has caused problems for lots of people - remnants of LW left behind. Use your computer's search to look for files & folders with limewire in the name & delete leftovers that way (just be careful...if your saved folder has limewire in the name then you could end up deleting your downloads as well!!!).

Lots of people also recommend CCleaner, to clean up after uninstalling.
CCleaner

Before you uninstalled LW, were you having problems with it opening by itself all the time & refusing to stay closed? If that's the case, your computer might be infected & you should scan your computer with a good, updated AV program. Check out the thread below for links to online scans & more info about the virus.
* WARNING: Viruses on network you should be aware of! *

If that doesn't help, you could try AVG Free AV & see whether that helps!
AVG free
Make sure to update AVG before you scan your computer.