Eric, I have actually an opposite opinion of the people above. Check out this thread:
http://www.toyota-4runner.org/showthread.php?s=&threadid=276&highlight=navi
Here's some more info:
http://www.toyota-4runner.org/showthread.php?s=&threadid=986&highlight=navi
TOUCH SCREEN is probably what sets Toyota and Honda NAVI units above everyone else. It is simply more intuitive and easy to use.
Another advantage is in mapping. For example, if i wanted to drive from Texas to Florida, the Toyota unit requires just ONE TIME programming. You set and that's it...it will direct you to your destination.
With the aftermarket units, you have to program it by region. For example, with the Magellan, you have to program it to go from Texas to Lousiana...and then program it AGAIN, from Lousiana to Florida. That is, you can't program it to map from Texas to Miami...it must be programmed at least twice! The Magellan hard drive divides the country into regions...and you cannot program it beyond one region. This limitation is NOT seen with Toyota (or Honda) NAVI units.
The other NAVI aftermarket units, such as StreetPilot, are PC-based. That is, you find a route that you want to take from Texas to Florida and then download it into the small hand-held unit. HOWEVER, you are limited! Again, because of the handheld's small memory, you canNOT store the whole route...so you have to break it down. That is, there's only enough memory in handheld to drive to the end Lousiana from Texas. Then you have to turn on your PC again (at a hotel or rest stop), and download the rest of the mapping instruction into your handheld unit. You may even need to do this more than just once if the route is long.
As you can see, these aftermarket units are STILL limited as compared to Toyota's DVD unit. In the near future, i am sure that these aftermarket units will overcome these limitations...but for now, they have not. Beyond all of the above limitations, the Toyota units are very fast compared to these aftermarket units.
From the first link above, only KENWOOD navi units are equivalent to Toyota's and Honda's in terms of ease of use and speed...because they are practically the same. Unfortunately, for the complete install, the KENWOOD unit will run around $3-4K, which is a lot more than what Toyota is charging! Alpine unit will cost about the same and does not have touch screen feature.
Lastly, i don't think you can change the destination while the 4runner is moving...this is where Toyota and Honda NAVI units differ the most.
In my opinion, if you NEED a Navi unit, then get one on your 4runner...you won't regret it! It's worth it! I wish that my 4runner came with that option in '02. My brother's Lexus LX470 has one...and it is just simply amazing. BTW, my other brother has the Magellan unit and it's good, but not nearly as good as the Toyota's unit. So, this is all from direct comparison.
Hope this helps.