Hello firearm1296. Your question is quite vague in that you've not narrowed it down to anything tighter than a 9mm auto. Unless someone owns a (very) broad selection of 9mm handguns, has had warranty issues with all of them and attempted to do some customizing... that's a tough question to answer fairly.
Based on civilian and LE sales, as well as the number of customizers on the net, "beeenbag" may be right in his belief that Glock is the "best" in the categories you've inquired about.
I've owned, among others, samples of all the guns listed below, but none ever had issues... so, from my purely subjective (if there's an objective one, I'd love to see it) perspective and in no particular order... Sig Sauer, Glock, S&W, CZ, Kahr and Springfield Armory all have good reps for service. As to the aftermarket... Glock, CZ, and Springfield Armory have, perhaps, more accessory support.
I own (mostly) 1911 pattern 9mm handguns... but I'm guessing that's not what you're interested in. The aftermarket is huge and after-sale service depends on the maker. Colt, Springfield Armory and Kimber are brands to consider.
Cheers,
C