First, be clear about what you mean. "Factory Toyota" may mean dealer parts to some and something else to others. I will use the Original Equipment Suppliers for parts they made such as:
Aisin: Clutch, clutch cylinder, fan clutch, water pump, fan bracket, many others
Denso: MAF, A/F and O2 sensors, plugs, A/C compressor, alternator, starter, ignition coils, and others.
Koyo: tension timing idler
NSK: center timing idler
Tokico: Shocks
I will buy the above wherever I can get them cheapest, usually Amazon, partsgeek, rockauto, fcpimport, or even e-BAy.
I also use NAPA/Wix for all filters, PCV valves and grommet, Zerex Asian coolant, brake pads, NGK spark plugs (OE), some drain and fill seals, headlight plugs and other universal electric stuff like relays. I use also NGK plug wires (not OE).
I have used Certifit for bumper parts and one front marker light(acceptable) and one headlight (bad move).
I just read through my maintenance log going back to the day I drove it home in 1999 and everything that has gone into the truck is covered above. I still have original rotors and drums but I would probably go with Brembo when I need those.