Assuming there is still a market for mp3 players by then and something new hasn't come along (advanced phones or mini tablet type things) I would wager the iPod line will eventually go entirely Flash based, there are new advances in flash memory all the time and it's not outside of the realm of possibility that there will be commercially viable 60+ GB solid state drives in the near future. I would also expect there to be a significant screen improvement, brighter crisper, maybe interactive in some way.
If the rumors are true about the video iPod being essentially a big touch screen, then that could become the future of iPod design, assuming people like it. As much as the iPod is defined by its interface and its click wheel, it's also about it's over-all ease of use and functionality.
I don't believe iPods will get TOO thin. I could see them conceivably getting about as thin as an iPod nano, but not much thinner than that.
I'd also be willing to bet that apple will revamp their headphones substantially in some way. I don't think they will go wireless or anything but they might redesign them to be far superior quality. They are already pretty decent now, but there is always room for improvement.
I can't really think of any whizbang features or innovations that might be brought to the table in subsequent releases, but if apple was using OLED or similar technology in the future it would be neat to see a faceless iPod where the screen(and/or buttons) kinda just appears on the surface, perhaps with some eye candy.
But all that is based more or less on a linear development of technology which, we all know is not always the case. there could be breakthroughs that enable radical changes in portable devices(high capacity rechargeable solar batteries or something like that)
That's also assuming that mp3 players even exist 5 years from now. It's not to say that people won't still be listening to music portably, but the consumer public might just as easily adopt a new toy as their portable media provider. I personally don't think the microsoft Origami is going to make a significant splash in any markets, but it's certainly possible. If that type of device becomes popular, then I'm sure the iPod will evolve into something similar.
and I'm sure that I'll sill be using a 3rd generation iPod in my car if I can help it.
But the other thing to consider, design wise. Apple really has a winner with the current 5g iPods, imo. Design wise, nothing *needs* to change. Apple doesn't usually like designs sticking around for too long, but they clearly have an exceptionally great design with the 5g iPod. So It might just come down to better battery life and more storage with new models.