I'm sure people more knowledgeable than myself will post up here shortly but I'll throw my $.02 in for now.
You already mentioned the head gasket. That seems to be the biggest thing to look out for on 3VZE (3.0 6cyl). Coolant/water in the oil and a sweet/coolant smell to the exhaust are indicators that the head gasket may have issues. You could have a toyota dealer run the VIN and see if the recall was every done. If the recall was never done, there are some people on here that have gotten toyota to do it even all these years later.
Other than checking all the normal things when buying an old used car, that's about all I can think of really. The tailgate window motor is a PIA is it's not working.
Pretty much everyone will tell you the 3VZE or 3.slow is not their engine of choice...it's under-powered and very thirsty in stock guise. You get better mileage and not much less power with the 4cyl 22re.
I picked my '94 up this past Jan. Mine is the 3.0 though as well and I can say that I haven't had any issues since I bought it other than only getting ~16 to 17 mpg. It had 111K on the clock and now has just shy of 122K. I've done the timing belt kit, full tune up, full brakes front and back, replaced leaking valve cover gaskets, headlight bulbs, one tail light bulb, and 3 oil changes...all normal maintenance and that's it on an 18yr old truck.