There are a handful of things that the dealer can change in the computer for you. If the OBD scan tool you have is able to write to the computer, you could make those changes yourself.
One of those things has to do with the active tire pressure monitoring system introduced on 4Runner in 2004. For Toyota, the sensor in each wheel has a unique transmitter ID. Those ID numbers have to be programmed into the computer in order for them to work. That's how the computer knows it's reading your wheels and not those of a Toyota parked next to you. A lot of people like to change to winter wheels so that their good wheels aren't damaged by road salt, but TPMS makes that more interesting because the sensors will be different. It would be wonderful if you could program the other set of ID's into the computer yourself, as it's expensive to pay the dealer's labor rate for their time.
The other big thing I can think of that would be nice to update is the Toyota Customizable Body Electronics settings, or C-BEST settings. Those are things like whether the doors automatically lock or unlock at certain times, whether the keyless entry beeps or not, or whether pressing the unlock button on your remote opens just the driver's door or all doors on the first press. Again, without the right scan tool that will write those settings into the computer, you have to have a dealer do it. There's a PDF file listing the 4th Gen settings
here. I don't believe 4Runners prior to 2003 had those settings.
Things that advanced are manufacturer-specific of course, and what you can do will vary by brand. If you're shopping for scan tools, you'll find that they all support a bunch of standard information that can be read out, and then you'll see some that offer optional add-ons that are specific to a brand.
Standard things that would work across all brands would be things like DTC trouble code read/clear, freeze frame data display (the computer saves a bunch of data at the same time it saves a DTC code that may help troubleshoot it), and real-time monitoring of a bunch of different parameters that tell you how the enging is running.
A couple of common brands of code readers you'll see in auto parts stores or even Walmart are
Innova and
Actron. Google will turn up many others, as well as other software tools besides those I listed above.