Have you changed the location of your saved folder at all?

Providing you haven't been saving files to within LW's program files (C:\Program Files\LimeWire) then you shouldn't lose anything. Some people mistakenly save their downloads within Program Files & in that case, uninstalling LW will mean that downloads are lost. It's also a bad idea to save files within C:\Documents and Settings\username\Application Data\LimeWire... because deleting LW's preferences folder would delete downloads as well.

To check where your files are being saved, in LW go tools > oiptions > saving. You'll see the location of your saved folder there.

It's always a good idea to back up your files, just in case of a system crash or other tragedy