This is the best analysis of the upcoming sandboxing requirements that I’ve read so far.
Examples of Mac Apps that will be affected include iTunes controllers (Tagalicious, CoverSutra), inter-app communication (Fantastical), apps that browse the file system (Transmit), system-wide keyboard shortcut utilities (TextExpander), file syncing, and backups utilities.
This is, in a nut, the biggest problem these requirements will cause. It affects more applications that I think anybody knows so far.
The App Store is, of course, Apple’s distribution channel. They set the rules there. But the exposure it provides to independent developers is priceless, and these sandboxing rules prohibit broad swathes of applications from the store.
It’s also worth noting that iCloud will probably only be allowed in applications distributed through the Mac App Store. Say, for instance, that Panic were to release a version of Coda for iPad, and that they wanted to enable the Coda family with the ability to sync Sites across devices. Coda has access to the entire system — it arguably needs access to a system’s worth of directories — so Panic would either have to restrict the directories it can access or they would have to roll their own syncing solution and distribute exclusively through their website. Neither outcome is ideal for Panic or for users.