Would you buy a PC from 2009 in 2012? Just know and understand what you're getting...
The ML350 G5 is simply an old generation product (active from 2006-2009). The G6 is newer. Both have been eclipsed by more modern options. So you're talking about a major shift in processing architecture (going from Intel 5400-series to the 5500 and 5600 available in the G6).
The machines look nearly identical in tower form.
They're both relatively quiet. The ILO 2 technology is the same between the two servers. The G6 will have Hyperthreading, Turbo Boost, more RAM options and be a better virtualization platform overall. The RAID controller and storage subsystem is a bit better as well. Keep in mind that the tower servers are no longer HP's primary focus, so the ML350 did not have a G7 equivalent.