Go_Gophers is solving your problem for the future. Reinforcing the default setting in iTunes should ensure that future downloads from the internet are in iTunes format (you may have to do this every time you upgrade Limewire or you suffer an OS crash — monitor the first download after either event).

But as to the files already downloaded which have been allocated to Quicktime, you will have to manually add them to your iTunes library or else you will always have to play each file individually through Quicktime.