Whatever preferences you set within LW's tools > options (eg saved folder location, connection speed, upload/download bandwidth etc etc) are saved within LW's preferences folder & these settings are remembered by LW until you delete the preferences folder. If you were to delete the prefs folder, you'd go through LW's setup wizard again on startup & you'd find that all settings within tools > options had reverted to defaults.

See below for locations of the preferences folder (named LimeWire).

For XP C:\Documents and Settings\your username\Application Data\LimeWire

For Vista C:\Users\your username\AppData\Roaming\LimeWire

This folder's hidden by default, so it's necessary to show hidden files & folders in order to find them

To completely uninstall LW start > all programs > limewire > uninstall. Now use the computer's search to look for all files & folders with limewire in the name. That will delete things like the preferences folder, which isn't saved within Program Files\LimeWire. Just check to make sure that your saved folder doesn't have limewire in the name, or you could end up deleting your saved files as well

If you like, you can also run these apps:
CCleaner

Microsoft Windows Install Clean Up

LW should be completely gone now.