You can in theory upgrade either to some degree. The 4,1s just kind of hit a sweet spot if you find a good deal on one, and they're likely to remain supported longer. Obviously I can't guarantee that, but the 3,1 hasn't been sold in roughly 3 years at this point, so it makes me nervous regarding longevity. Ram is way more expensive, and this becomes more noticeable if you're going to max it out. The 1,1 ram is a little cheaper, and some people have used it. The 4,1 ram can go as high as 32GB without being terribly expensive, and at that point it'll satisfy an extremely high percentage of computer users. Part of the appeal of the 6 core thing is that it's clocked much higher. Not everything scales in a linear manner with core count, and per core the performance there is quite good.
I've seen quite a few mac pros on Craiglist. When we see new ones that number will probably go up.