Hi,
Just to re-cap:
I ran a full format & restore from the recovery media; When I reinstalled the applications (none of which are pirated versions) apps started removing themselves again. I disconnected the firewire drive I use for Timemachine (as per a request in the thread) in case it was the reason for removing my apps and started to use the mac again.
Within a day or two, I was missing a few new applications - App Zapper went, Adium went, Itunes went. Poof! This time I had no Timemachine, so I had to reinstall the apps again from scratch.
I ran 'another' full format & recovery but this time never once connected the unit to an internet connection (disabled wireless and did not connect a patch cable) And continued to use the unit in the normal manner - albeit, without any updates, Adium, and any other internet based apps.
.... a few days later, my full Adobe package is missing again - whilst I was using the application! Could not save file - so had to quit without saving, upon attempting to re-open, all Adobe software was gone
So, I think I've ruled out trojans, timemachine, hard drive, ram.
I think it's time to bin this macbook pro and buy a new one. damn.