Here are some examples of post rotation procedures. Obviously this is only a sample, you'll need to search for each car's procedure until you know all of them by heart.
2005 Acura MDX

Rotate tires, set pressures, you're done.

The MDX has an initiator over each wheel to activate the TPMS sensor, so it self learns tire position. Pressure thresholds are set in the TPMS ECU using the HDS scanner. There is no need for pressure or position learning after a rotation.

You must set the pressure according to tire placard unless you change the set pressure in the TPMS ECU with the Honda scan tool. However, if this is done (to accommodate different tires), you should make a note near the placard so the customer does not end up with a tire pressure warning light every time they get an oil change.
2008 Honda Civic

Rotate tires, set pressures, you're done.

The Civic does not monitor tire position. Pressure thresholds are set in the TPMS ECU.

You must set the pressure according to tire placard unless you change the set pressure in the TPMS ECU with the Honda scan tool. However, if this is done (to accommodate different tires), you should make a note near the placard so the customer does not end up with a tire pressure warning light every time they get an oil change.
2006 Toyota Prius

Rotate tires, set pressures, press & hold TPMS reset button w/ KOEO or READY until the TPMS warning light blinks 3 times at one second intervals.

If the reset procedure is not done, or not done properly, the TPMS light will come on after the customer has driven quite a distance from the shop (~20 miles or so).

Pressures thresholds are set when the reset is performed. Tire position is not monitored.
2006 - 2007 Toyota Rav4

The only Toyota without a TPMS reset button so far.
Rotate tires, set pressure to placard, you're done.

Pressure thresholds are factory set and not adjustable. I have not found a way to change the pressure threshold with the Techstream, so replacement tires will need to be carefully selected to meet the Rav4's load requirements at 32 PSI.
2007 Toyota Corolla

Rotate tires, set pressures, press & hold TPMS reset button with the engine running until the TPMS warning light blinks 3 times at one second intervals. KOEO WILL NOT WORK!!

If the reset procedure is not done, or not done properly, the TPMS light will come on after the customer has driven quite a distance from the shop (~20 miles or so).

Pressures thresholds are set when the reset is performed. Tire position is not monitored.
2004 Nissan 350Z Set pressure & you're done. No rotation possible due to different sized front & rear tires. Pressure thresholds are set in BCM. No reset necessary after resetting tire pressure.
2008 Nissan Altima Hybrid

It appears that rotating & setting pressure will be all that's required. Nissan does use an activation tool and learn mode, but it appears there is no tire position indicator for the driver, so learning after each rotation seems pointless. I may revise this later once we've seen a few come in.
A few examples of how to register a new TPMS sensor.
2008 Camry Hybrid

Use the MasterTech or the TechStream to display all registered TPMS sensor IDs
Write down all of the IDs (or print with the TechStream).
Install new TPMS sensor & fill tire
Deflate tire more than 6 PSI in 30 seconds
Use scanner register all sensors
2008 Honda Civic It's worth noting that the new Hondas seem to be moving away from their "initiator type" TPMS, that uses an initiator mounted over each wheel to track location. Most of the new models do not have the initiator, so before you register a new sensor, you'll need to figure out which sensor is bad. Finding & registering TPMS sensors seem to be the only official use of the TPMS tool for Honda products so far. To find a TPMS sensor, the HDS is connected and put in to the "TPMS Position Check" mode. The sensors are activated one at a time with the TPMS tool. When a sensor is activated, it's ID is displayed on the HDS so you can determine its location. Once you've found & replaced the bad sensor, the HDS is put into the Sensor ID Learning mode, and all 4 sensors are registered (regardless of how many are new).
2005 Honda Pilot The Pilot has initiators over each of the wheels. If a TPMS sensor is replaced, just hook up the HDS and perform the memorization procedure. The initiators are used to activate the TPMS sensors, so no TPMS tool is needed.