* If you hooked up a clock to rapidly pulse a move command which moves the player very slightly in a direction, you could simulate a powerful wind - this could be an interesting challenge in parkour.

* It may seem silly, but you could make all players in the world "jump" with 'move @a 0 1 0'. Or, if you're a sadistic admin, 'move @a 0 10 0' can provide some entertainment value.

* With 12w38a, you can add selector arguments, for example limiting a command block's search range. If you set a block to 'move @a[r=5] 0 0 1', it effectively becomes a forcefield, pushing any player within 5 blocks of it southwards. This is not much of a 'practical' forcefield (a practical field could simply tp the person outside of the range), and more for fun/challenge: a player may be able to dive deep enough into the field to flip a switch and shut it off, if they have Swiftness II status, for example.

* You can make a world map wrap around itself. For example, if you're familiar with many older Japanese RPGs, if you go off the north end of the world, you're sent to the south end, and if you go off the east end you're sent to the west, etc. Ignoring that this isn't topologically possible on a spherical planet, it would be interesting to make your Minecraft map endlessly loop. Of course, you would have to copy a small bit of the world on each end to seal the deal in this illusion :P

* You can have a black hole. This is similar to the forcefield, but a little trickier: you can have more commandblocks with smaller radii, so that the closer a player is, the more commands pull the player towards the center. You would also need a set of command blocks for each side, as the player must be pulled from a different direction depending on where they are. If you don't bother with trigonometry, and have four sets of command blocks (one for each of the cardinal directions), your black hole will have a four-leafed-clover shaped area where it sucks players in. Fortunately, I doubt it would be a noticeable flaw :P. Remember that 12w38a's selector arguments mean your command blocks don't have to be anywhere near the black hole, so the redstoning shouldn't be too complicated.

* You can have an antigravity area, or even a low-gravity area, by moving a player slightly upwards. If you've played Quantum Conundrum or seen people play it, you may be familiar with the idea of constantly flipping gravity to glide across a gap - well, now that can be in Minecraft too. (Disclaimer: you can't ride on a safe or box, you'll have to go on your own :P)

* Simulate an earthquake's tremors by moving all players randomly with many command blocks. The randomness part has to be done with redstone, of course, deciding which blocks to activate.

* Interactive flipbooks/battles/cutscenes/whatever-your-heart-desires. First, check out SimplySarc's video proof of concept for interactive bosses in Minecraft.
      * Now, there's only one notable limitation to this awesome idea: The player is always sent back to a specific location. You couldn't, say, have a player running away from a gigantic meteor (made of blocks) that's about to fall and crush them. If you could move the player to the same location in the next frame, rather than some fixed spot, they could actually run around freely and it'd be a lot more interactive.
      * Of course, this command gives you the power to do just that! Better yet: if the player doesn't get out of the way of some large falling/moving object, they'd effectively get teleported into it, taking suffocation damage for as long as that frame lasts. Fill the inside of that giant meteor/hammer/fist/train/whatever with lava if you wanted it to be a rapid death. Suddenly, your boss fights can have more attacks than your typical Minecraft attacks, and the only limit is your imagination.
      * Of course, this doesn't have to be limited to battles. You can try to survive an animated earthquake, or have a party with a working disco floor. Really, I look forward to maps doing this sort of stuff.