If you want to take a vehicle to Shetland, there are two ferry options:
1. Northlink Ferries from Aberdeen – Lerwick.
2. Northlink Ferries from Kirkwall – Lerwick.
Both are in fact the same service, but not all ships stop at Kirkwall – some go direct from Aberdeen-Lerwick. If you are going direct to Shetland from anywhere south of Inverness, the Aberdeen-Lerwick option probably makes much more sense than having to take a separate ferry to Orkney and wait around for the Northlink service to Shetland.
The Kirkwall-Lerwick service, which we used to get from Orkney to Shetland, leaves Kirkwall at around 2330 and arrives in Lerwick at about 0730 (June 2010). Cabins are optional (£80+) and reclining sleeper seats are available at no extra cost for the budget conscious (us). Aside from a few well-lubricated souls who bounced in around 0200, the reclining seat cabin was peaceful enough to get some sleep.
I would add that this service isn’t really much fun if you don’t like ‘the motion of the ocean’. The crossing is often a bit rough – note in the picture below how the chairs in the dining area are tethered to the floor!