i can’t really lend advice for the graphics cards because i havent been able to test different ones.
i have 3rd party RAM and Hard Drives in my G5s and i’ve never had an issue with AppleCare. they consider them user-upgradeable parts so it doesnt affect the service. a good Seagate or Maxtor server-level hard drive has a 5 year warranty, and the RAM from OWC is half the price of the Apple store for the same brand. so it seems like a no brainer to me. i understand those who want the all-in-one Apple solution for simplicity, but with a fully loaded Mac Pro, your talking hundreds to thousands of dollars difference.
also, if you buy 3rd party RAM, get the non-ECC. ECC is only needed for scientific and math intensive systems. the fact that Apple only sells ECC RAM now is probably the reason for the large spike in RAM costs. its not necessary IMHO.
e