ThinkSecret claims that Apple will be pulling poor sales performance software items from their stores to free up space for higher profit items.
Beyond this, as of July, Apple is planning on pulling non-Universal binary software to provide customers with a more consistent software experience. Owners of the new Intel-based Macs will have much better performance with Intel native (Universal) applications than with PowerPC native applications.
Apple, however, will make an exception with Microsoft and Adobe software -- as neither company is expected to have native versions of their software available by that time.