Personally, I think it's really hard to choose the right package, and the decision is ultimately a personal one.
Here are some thoughts based on my experiences:
I have an 05 Tideland Pearl Prius, and love the car!
I got it with #5 package.
The JBL stereo is a huge disappointment. In my view it cannot even hold water to most stock stereos in other cars. My pre-Prius car was an 03 MINI Cooper S. For $550 I got the Harman Kardon premium sound system, and it absolutely rocked!
JBL: absolutely not worth even a single $!
I could easily live without the alarm.
Probably not worth the extra cost!
The auto dim mirror is great, but as you pointed out, you can get them aftermarket.
Worth some money, but not the cost of the package.
I still don't like the Smart Key System. Mostly, because it's not as smart as it could be. If it could recognize when I leave the car, and lock the car automatically it would be worth it, but otherwise I would be just as happy with a remote control FOB.
IMHO not worth the money as is.
Side /head airbargs: most definitely worth the money!
You can get them on their own as package #1.
I now wish I had chosen a different package, but still not sure which:
I am not sure about VSC.
I had the MINI equivalent in my MCS (called DSC), and it did kick in a single time during my 2 years, 45,000 miles. Maybe it saved my bacon at that time, I don't know. The MINI handled so well I felt like I did not need it. The Prius drives nicely, but handling can't compare to a car like the MINI, and so VSC may become more important.
I had Xenon headlights on the MINI, and don't have them on my Prius. Surprisingly, I don't miss them, and I think the halogens on my Prius give ample light. The Xenon's are brighter, but have a much sharper cutoff, which made me readjust the auto-leveling feauture on the MCS quite often, as they were frequently aimed either just a little too high, or a little too low. Halogens are not as finnicky in that respect.
My MCS also had front fog lights, I think they are just a fad and essentially useless, and would guess the same to be true on the Prius. I think I might add my own aftermarket foglights at some point.
With respect to NAV I always felt if you really need it you could get an aftermarket NAV system for 1/3 of the price, and use it for other purposes such as in rental cars etc...
Ultimately, I wish Toyota would move beyond packages, and allow buyers to custom select package components, just like MINI does.
If that were an option, I would get and only get:
Side airbags
VSC
Auto dim mirror
My 2c worth.
M