both use the same engine (u didn't mention the year so could either be M54 or N52) & gearbox (probably 6hp26 or 6hp19). However other parts like the lower arm, control arm, absorbers,etc the e65 should be more expensive. The other thing my mechanic mentioned to me is the speedometer for the e65 is a bit problematic, not sure what he meant, but I wasn't really interested in the e65 so I didn't probe further.
I too had a similar dilemma, in the end I went for a 530d. I am not a fan of the e65, cannot stand the shape. The e60 with m5 or msport bodykit still looks good.
My advice is go check out both cars yourself. If you like then go for it!