An app is loosely defined as an ordered collection of tabs which users can select 
from the Force.com app menu in the top right of the screen. 
With the Summer '12 release, we've added tab and app settings to permission sets.
This means that permission sets can now control:

• user permissions
• object permissions
• field permissions
• Apex class access
• Visualforce (Apex page) access
• tab settings
• app (tabset) visibility settings

This means that when creating new apps on the Force.com platform, you can start 
thinking of the 'functional roles' a user might need to work with that app. Working 
with that app, a user could be amanager, a coordinator, recruiter, a clerk, order
entry, warehouse stocker, post master, claims adjuster, procurement officer, 
administrator, or just a plain old 'user'.
By separating a user's function tied to an app, an administrator removes the 
overhead of trying to figure out which profiles they need to create or modify in 
order to address all of the unique combinations of rights users may have across 
all of the apps they are assigned to.
This works best where the app has simple layouts and record types, as those access 
controls are still only available on a profile. But if you can create a permission set that 
represents a user's functional role tied to an app, you can remove some of the challenge 
with ongoing app-specific changes to a user's permissions.