Interesting thread. Really enjoyed Neapolitan's and innerspaceboy's posts on the first page.
I actually had the 'importing of consciousness to a computer - is it you?' conversation somewhat recently. I'm of the opinion that organic responses to stimuli are what link the brain to reality and without capturing that, you're really just 'backing-up' your experience up to the point at which the procedure occurs. The idea of living in a purely mental world, unbounded by the body's needs, is fascinating, however. As a general pessimist, I subscribe to the Golden Throne theory of artificial life extension (from Warhammer 40k). Essentially, the Emperor has lived in a realm of pure mind for the past 10,000 years and his humanity is completely stripped (side note for 40K fans, TIME OF ENDING - SO COOL!); this does not bode well for the trillions living in the Imperium. The drudgery of human existence, cooking food, walking down a crowded street, small talk with family, going to work; all of these things constantly reinforce an understanding of the transience of existence and engender empathy for our fellow man. I'm not sure how HAL 9000 (or I guess in my case, RAR 9000) would relate to humanity once stripped of its requirements.
A slower integration of mechanical/digital organs/synapses raises a different set of philosophical questions. I have yet to see Ghost in the Shell (either the anime or the apparently terrible recent film), but I understand it's more or less exclusively about the Ship of Theseus paradox (plus violence).
Ship of Theseus