The built-in nav system is a really nice system, especially since it adds the rearview camera and support for a Bluetooth-enabled phone (use the stereo as a speakerphone, and dial from the nav system). But the drawback is the price. It's expensive up front, and believe it or not, it adds very little value at trade-in time. I've traded in two cars with nav, and the nav only added a few hundred bucks to the value.
Pros for the factory nav:
+ Huge screen
+ Always on (no messing with unpacking it and plugging it in to use it) - that's really great if you have a long commute and might use the map on a regular basis
+ Good software (Toyota and Honda are consistently highly-rated for OEM nav)
+ Backup camera
+ Bluetooth (if you have a Bluetooth-enabled phone; I don't)
+ It's a bigger screen for radio controls, disc changer, song/disc titles, and other info
+ Through a "hidden" service menu, you can run self-tests and pull OBD codes from the main car computers
Cons:
- Expensive up-front
- Expensive map update discs
- The software can never be upgraded. You can get updated map data, but you'll never be able to upgrade functionality (unless you actually change the computer hardware, too)
I didn't get nav on my 4Runner because it was only being offered on V8 Limiteds, and I didn't have the cash for both the V8 and the nav system. But I think I made the right choice getting the V8 and letting the nav go. I bought a Garmin StreetPilot 2720, and I'm very happy with it. I have a short commute to work, so I don't need a map every day. I actually think the Garmin software is better than the nav software from 2004; the Garmin software is more oriented toward where you're going as opposed to where you are. You'd think that a 3.8" screen is terrible, but it's not. You really wouldn't want anything bigger sitting on top of the dash, and the Garmin 27xx/28xx series uses the screen space pretty efficiently. There's something to be said for the portablity; I have two cars, so I can use the Garmin in both, and I can take it into the house for software upgrades, adding marked points, and pre-planning routes.
I do miss the backup camera, but I made sure I got a V8 without the JBL audio upgrade so that I'd have the mirrors in the back of the truck. The mirrors aren't as nice as the camera, but they're better than nothing.