SP 1 for App-V 4.6 is around the corner, and has some significant improvements.
Check it out: http://www.msteched.com/2010/Europe/VIR304
App-V is not only suited for avoiding application conflicts, but also helps you to deploy applications faster to your users, and is also a must for developers and testers, for testing the same application but with different versions on the same machine.
I`m looking forward to test SP1, and give you some more details about it.
Remember that though the sequencer in SP1 has many improvements, it is still important to documenting the process. I have experienced that I often have to do the sequencing over and over before I`m happy with the result, and if the application requires lots of testing before deploying it, be sure to keep your notes and also share them among the rest of the sequencing-personal.