I've never owned the 3.0, but I hang out with a bunch of guys on another forum that do, and this comes up all the time, so I'm almost an expert.
The big knock on the 3VZE is the head gaskets... they ran the exhaust too close to the engine head right near plug 6. This leads to fairly common gasket failure, but it's hit and miss - I know guys that have 300 on the clock and the original head gasket, others have had multiple failures. Other than that, it's a very reliable engine. It's not very powerful (and it's pathetic when paired with the slushbox a340h automatic), and it's obviously worse on gas than the 4 cyl 22re that was the other option in those trucks.
On the plus side, if you drop a little coin into aftermarket headers that go under the engine, you almost eliminate the head gasket worries, and other than that it's a very reliable engine. It is more powerful than the 22re, and it's supposed to be a very simple swap to the newer 3.4 v6, which is as bulletproof as the 22re and twice as powerful. I drive a 22re, and if I were going to buy another Yota I'd get something with the 3.0 and a manual, and just plan on swapping to a 3.4 if/when the motor blew.