Most of the programs available with Limewire are crap. Half are infected (hence the security warning). Half are freeware or shareware.
You're not trying to launch the program from within Limewire, are you? That will give you a security warning as well.
If you choose to download programs, make sure you scan them before you open them. Avoid .exe files for sure.
Good Luck
Dan
P.S. Keep a close eye on the file size. Does it look appropriate for the program you want? Avoid programs with small sizes.