Before you ever uninstalled LW, was it popping up all the time (not just once when you turn on your comp, but every couple of minutes)?
If that was happening then there's a good chance that you're infected. In that case, try the fixes in the link I gave in post #2.

If there was no popping up of the original LW, you might just've stuffed up the uninstall (don't use Add/Remove Progs...uninstall via Start > All Progs > LW > use the uninstall option).

Open Task Manager, click on the Processes tab. If there's any LW process running, end the process. If that's not the answer, use the computer's search to look for all files & folders with limewire in the name & delete what you find, you could also try using CCleaner - Home.
*If you've changed any saved/shared folders from the defaults,or have any saved/shared folders with limewire in the name, make sure that you don't delete those folders in the process!!!*

Next, delete LW's preferences folder when LW's properly closed. See point 3 here & also point 2 if you've used older versions of LW in the past (there could be a folder in either location).
Fixes for LimeWire
This will change all of your settings within options, you'll have to go back through afterwards & reset things. If you're not sure of your settings, go through LW's tools > options & write them all down, so that you can reset things later.

Last of all, reinstall LW. I guess you have Pro?