While most Prius parts are Toyota proprietary, and Toyota in general uses more or less the highest quality parts in the world, there are a few cases where aftermarket parts may either meet or exceed OEM quality. What comes to mind for me are 12V battery: Optima D51 with terminal conversion HID bulbs: Philips Belt, Hoses: Gates O2 sensors: Bosch Tires, brake pads: Many choices, subject to personal performance requirements Any other examples of what works, or better yet, what didn't work or what wasn't worthwhile?
In general, I am not a fan of aftermarket parts. I've had prior experience as an owner of other vehicles where I thought I might save $ by buying aftermarket, only to find the part had the wrong fit/function, did not have the service life I expected, etc. I've wasted enough time with the wrong part to resolve "never again". In the distant past I owned European vehicles (Mercedes-Benz, BMW, and Jaguar) and the parts markup at those dealers was sufficiently high so that there was an economic incentive to look for aftermarket alternatives. However, my policy back then was to buy aftermarket only if the part was made by the original equipment German manufacturer - in other words, the same part as installed by the auto factory, but without the MBZ, BMW or Jaguar markings. Regarding the Prius, I would say that maintenance and repair parts are generally priced at reasonable levels if you place weborders at places like toyotaworld.com. Therefore I haven't found a compelling financial reason to look for aftermarket parts. My experience is that Toyota parts are generally of high quality so I don't have a performance motivation to look for aftermarket parts. HID bulbs would be one area where for price and performance reasons, owners are motivated to look for alternatives such as Phillips. I would agree with the consensus opinion that Goodyear Integrity tires are not the best choice. Other than that, my personal preference is to buy the correct Toyota part for the other categories in your list above, as I don't see a strong economic or product performance reason to buy aftermarket.
If the after market parts are American made, I would consider that a good reason to use it, provided they are good quality (i.e. Gates)