A few advantages of U3, off the top of my head:
1. you can download apps with a click of the mouse (nice for ppl who are time constrained, not so tech savvy, or lazy, like me

)
2. everything is then pickable off a familiar windows style menu
3. you know the app has been through a certification process to check it is correctly engineered to the U3 standard
Plus, you can use your drive for applications or as a regular flash drive (just data storage) as you choose, which gives you great flexibility and adaptability.
Elly