NeXT has been down this road before. Original Cubes and Slabs were based on Moto 68k chips. Eventually NeXT sold hardware division to Canon and ported to generic PC hardware. The Application Wrapper layout is explicitly designed to support "fat binaries".

Upon purchase of Apple for negative money - NeXT ported to PPC. The two ports have pretty much guaranteed that the source code is absolutely squeaky clean. To keep it that way, Apple's internal build scripts continue to build the code for all architectures to surface portability problems. This is the 5 year double life that Jobs referred to.

How do you make a fat binary? Check a checkbox in the IDE and the build environment will build one. For most apps this is literally just a recompile. Already the dev lists are full of queries from new developers and the old timers are explaining how it worked on the last transition from black to white hardware. The only ones to be screwed are developers of high end "PRO" apps for image and audio processing that use the AltiVec instruction set or hand tune their assembly for performance. It sounds like there is an emulator for these instructions for the short term.

The other key issues will be stuff that puts data on the wire - there is a set of API's for dealing with this that have been there forever (although I suspect have been ignored lately since they do nothing on PPC) called NSByteOrdering. They're pretty easy to use and shouldn't take too long to fit into existing code. Certainly it can be done before the first Intel-o-Macs ship.

So key takeaway is "this road (and this OS) is very well traveled" and I would expect you to never notice a problem. Purchase with confidence.