Ok some clarification is needed up in here. A manual transmission is just a bunch of gears with special mechanisms built into the hubs of the gears called synchros that match everything up while shifting. The weak points in a manual transmission are these synchros, the clutch, and followed by the the mechanical limits of the shafts. As far as upgraing a manual goes you can change to a synthetic fluid like redline MT-90 to helps the synchros and bearings last longer and work smoother, and upgrade the clutch to prevent slipping that causes them to burn out. Clutches are rated by the max rpm the can handle and the maximum torque they can hold without slipping.
As far as automatics go there are many more parts and much more to upgrade. unfortunately there is little on the aftermarket right now to support our cars. Automatic transmissions have a torque converter where the clutch would be on a manual car. they also have MULTIPLE clutches inside the geartrain. Torque converters buldge out with increased power levels, run hot, begin slipping, and go bad. They are basically a fluid pump(a lot more complicated than this but it will do) so changing out to a good synthetic fluid helps, as well as adding a cooler to keep the temps down and combat thermal expansion of the metal parts. The cooler also helps maintain the seals and clutches so it is one of things that must be done to an automatic transmission that is going to see more power. When available, changing out the clutch bands and plates with those of a better compound (think racing brake pads vs. stock) will greatly improve the torque holding capacity of the transmission, as well as changing out the springs to improve the shift speed and quality. Think of this step as getting a complete transgo shift kit and rebuilding the transmission all in one step. Then to further improve shifting and torque holding capacity modifications to the valvebody (think the heart of the automatic transmission, it controls where and how much hydrolic pressure is sent to change gears) are made to increase the pressure on the the clutches, and apply that pressure faster to prevent slippagge that can burn out your clutch packs, allowing the transmission to hold more torque. Finally due to complexity, an automatic transmission has more parts shoved into a smaller area than a manual transmission, so many of the parts are thin walled and have tiny shafts running through them meaning they can't hold as much power as the big solid gears in a manual. If you are making serious power you may need to upgrade some of the planetary gear sets and most notably the input shaft that the torque converter spins, to thicker stronger versions.
Cliffs notes: For a manual get a synthetic fluid, a good clutch and flywheel, and don't abuse your synchros by powershifting/not using the clutch/being an idiot.
For an automatic: Fluid, cooler, torque converter, Valvebody modification, new clutch materials, hardend input shaft, stronger planetary gearsets and drums.
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