The MPC1000 is a standalone midi sequencer, sampler and performance unit all in one while the 'MPD24 with software' requires toting a computer along every time you want to play outside your home base with all the fragility and instability that a computer brings with it.
If you are working on a project that will never require mobility I would go with the flexibility and expandability of the 'MPD24 w/PC apps' option.
But if you can ever envision a time when you might want to take your music a-travelin', I strongly recommend you start with the all-in-one MPC1000. With the 2.0 software released earlier this year you can get a $40 caddy and mount up to an 80 gigybyte hard drive inside the MPC. Once you get to know it well you'll be flying.
I have both and prefer the simple, bullet-proof approach of the MPC over the frustration of working with even the best software. The ability to store data on a PC or Mac makes it doubly useful and the ability to process stuff inside the computer and then put it into the MPC for performance doubles it again.