Well, you were right, I deleted the package receipt and reinstalled Java and Limewire is working as normal again. I would like to know how Java was broken as well...
I would not have had any sign of this, as my web browsers (Safari & Firefox) displayed no signs of any Java error, nor was anything reported, and websites seemed to be functioning as normal.
Like I said, the last thing I remember doing before Firefox broke was installing the Quicktime security update. I doubt that would have broken Java but it was an HTML Java fix (hence HTML engine failure).
Actually, I did have a user account error not too long before, however, that revolved around some 'broken' files which were promptly repaired by the OS (although waiting for login to happen was a pain).
Anyway, thanks for your help. Limewire's working for me again. Really appreciate it!