Searched here for this and came up empty.

There were alot of hits on a Google search about this.
What brand and version of hardware and software do you have if you are running OBD II on a laptop?

I'd be interested in this, too.

Important additional question - does your software handle extended manufacturer codes, in addtion to the generic P0, P2, P3, B0, B3, C0, C3, U0, and U3 codes? By "handle", I mean "display"; I don't care if I have to look up the extended codes in the service manual, as long as it will report and display them. I don't see why any code reader can't display any code, but none seem to mention it.

There is a LOT of stuff that the Toyota will throw a code for that would be in the "manufacturer specific" ranges. For example, the tire pressure system DTC's start with C2.

Also, I've seen that some of the software packages support raw hex data streams to the car computer, with a raw hex result coming back. That's the kind of feature you would need to change C-BEST settings or make other config changes in the computer, assuming you can find out what data streams the Toyota scan tool is sending. Has anyone seen specifics for Toyota in this area?

I have wasted many nights researching this. I have a ProScan: http://www.myscantool.com/
I like it. I have played with it for hours. However, it really helps to have someone in the runner with you as it is hard to push the Start & Stop buttons as you drive. I bored my wife to tears one morning! I still spent hours in the driveway recording stuff for baselines. That way, if I do experiece something like a drop in mileage or misfire issue, then I can go back to my saved data/graphs and co-plot them on Excel to see what has changed.

It will not record specific manufacture codes. These are priority codes that the scanners do not recongize for some unkown reason to me. You could however pay for a better scanner. But it will kill your wallet. For $ 150 this is a fine geek-toy.

Give me some time and I will post a few graphs that created.

Oh another crude but very powerful bit of software is from this: http://obddiagnostics.com/index.html I came close to buying this one as I did not want to spend too much money.

The article below is excellent. It goes into the proceedure of geek-trouble-shooting with a scanner.
http://www.4x4wire.com/toyota/4Runner/tech/OBDII_ECU/

This was to compare the mass air flow with & without an air filter. The purpose was to determine if something like an aftermarket air tube is valid. In other words if I see no difference in air flow by removing the air filter, then there is no way that any device can create something that is not available in the first place.

However, my tests were done in the driveway while the vehicle was parked. The scatter in data is me trying to hold the gas pedal steady at different rpms. A better test would have been to actually drive the vehicle with & without the OEM filter in place. Also it does not take into account for less bends in a different shaped air tube.

I actually co-plotted the two different test runs but I lost the plot and I am too busy to do it now. But take my word, for these two tests there is no difference in mass air flow.

The ultimate test would be for some to compare the mass air flow of a stock setup and then compare this to someone who has some like a FIPK installed. I have a strong feeling that there is no difference! But that needs to be proved by experimentation and not reading the back of K&N

Here are two more: CTS coolant temperature sensor (blue-line degrees F & pink line degrees C) One can see a change in slope at 120 F. This is probably the thermostat opening.

And idle speed. The test was starting with a cold engine. I waited for the thermostat to open for a few minutes before terminating the test.

I feel like this too. Thanks for all the info.
Great minds think alike: I want to get some baseline data but also get a tool that will grab the extra codes.

http://www.obd-2.com/

Take a look at the hardware/software at the website above. It will take a bit of effort to figure out the website and what you would need, but it might do what you want at the best price.

Anyone have experience using diag-tools from TIS?