The media event at which the SDK was announced made it explicitly clear that there would be at least two "big ticket" features added with software version 2.0. One would be the ability to interface directly with a Microsoft Exchange server. The other would be the new Apps store.
It was specifically stated that registered participants in the SDK program (who had paid their $99 registration fee) would be able to submit as many software titles as they wished to Apple for distribution to end-users through the new Apps store.
The price charged for the software at the storefront would be entirely up to the developer's discression - even $0.00 if they so wished. Apple would take a percentage of the monthly sales revenue, if applicable, and forward the rest of it to the developer. It was also stated that this would be the only authorized means through which SDK-developed applications would be allowed to be delivered to end-users.
It was also specifically stated that these developments were meant to be applied to both iPhones and iPod Touches, but that iPod Touch users would have to pay an upgrade fee before the Apps store became available to them.
So, to answer your question... Apple will act as a gatekeeper, prohibiting software that violates their guidelines from being distributed. It's possible that some of the software you may be able to use on a Jailbroken iPod Touch may not be permitted through Apple's official distribution channels despite the technological feasibility.
For example, at the moment it looks as though this would mean most 3rd-party IM software (which, in order to be practical, would violate certain design guidelines restricting permission to run in the background) would be prohibited.
On the surface, it would appear that spreadsheet programs having the ability to compute inline formulae or run macros would also be prohibited. With a literal interpretation of the design guidelines, games such as Quake whose levels are interpreted from extrenal scripts, might be subject to prohibition as well.
Of course, those guidelines are always subject to change, especially given the fact that the SDK program is still in beta at the moment. As well, Apple would always have the right to negotiate case-by-case exeptions to certain design guidelines, especially for larger well-established developers like AOL or Microsoft, if certain programs which would otherwise be prohibited, are viewed as potentially useful or lucrative enough.