I ended up thinking of a few ideas for some new items:
An Item Cloaning Machine - Obviously, have it made from some very rare matirials - maybe a box of diamond and obsidian, with some redstone in the middle. Have it powered by redstone, a bit like with coal and a furnace, but the ammount of redstone needed is rellitive to the item - say, 1 redstone could clone 8 pieces of coal, but you'd need maybe 10 redstone to clone 1 diamond.
A Cyrogenic Prision - Maybe a box of iron with some glass in the middle. Pretty much like a bed, but minus the chance of waking up with a zombie bashing your face in.
A Telepor' Teleporter - I know, I know, we have the Neather, but wouldn't it be nice to not have to wander through that place? Like the cloaning machine, have it made from very rare matirials - a piece of diamond between a U shape of obsidian, maybe. Have each one link to every other - so say you placed three of them. going into the first build would take you to the second, second goes to third, third goes back to first. I think it could work.
To be honest, there really isn't that much missing from it - you could very well sell it as a full game as-is, or at least I think so. Of course, since it's still in Beta, it gives us a chance to surgest new ideas and solutions.