there are different grades of cv's sold at napa. the remanufactured can be either grade as i have found, but most often are an oem unit that has been refurbished, i don't see how they differ from stock, except often you have to reuse your dust seals by tapping them off the ends of the unit you pull off, or reorder from toyota. the new napa manufactured cv's are where i hear a lot of issues. i have two of them on my tacoma, and use my oem's as trail spares as was suggested. they are not bad from my experiences, but others have said they have less range of movement. the most recognizable difference from oem is the tulip joint (the side of the cv closest to the differential) is smooth all the way around on napa's brand, and the toyota originals are flat in three equidistant spaces, look kinda triangular.
the other difference is cost- a remanufactured cv is far less expensive at around $60 after the core refund - before the core, it's around $210. the brand new napa brand is around $150ish, and you keep the one on the truck. the third option i wish i would have gone for originally is to go to toyotapartsales.com and order a factory refurbished oem cv for around $150 before shipping, thus keeping the others as trail spares as was suggested by other members.
the only thing that is nice about going to napa or autozone*, is you get a warranty for a replacement which a lot of guys take advantage of. napa's warranty on remanufactured cv's is a 3 year, 36,000 mile warranty, and for a brand new is limited lifetime. autozone's policy is limited lifetime on remanufactured.
*napa and autozone get their remanufactured units from the same distributor, at least down here. i just found this out by trying to find one with dust seals on the ends, and they came in the exact same box at both stores.