to my knowledge (some of these are obvious, correct me in I'm wrong on anything):
battery size - factory only
performance upgrade - factory only
paint - factory only (but I guess any paint shop and turn it into any color you want aftermarket)
roof choice - factory only
21" wheels - can be swapped post-factory (needs to be done at service center b/c of tire pressure monitor system)
interior - factory only
tech package - factory only
sound studio - factory only
suspension - factory only
rear facing child seats - USED TO BE ABLE TO HAVE IT DONE POST-FACTORY BUT IS NOW FACTORY ONLY AS OF LAST WEEK
parcel shelf - can be added post-factory
paint armor - can be added post-factory BUT costs a lot more ($1450 vs $950)*** (see note at bottom)
HPWC - can be purchased post-factory but you need to have dual chargers for this to really work
twin chargers - can be added post-factory BUT costs a lot more ($3600 vs $1500)
supercharging (for 60kWh) - factory only (not possible for 40kWh, and included on 85kWh)
***PAINT ARMOR
like above poster mentioned, many ppl do not like the factory installed paint armor for various reasons. By default it is HALF HOOD COVERAGE. if your car isn't spotless, you'll easily see a line across your hood. if you want full hood coverage, I think its possible to contact Tesla and their installer and pay something like an extra $500 for full hood coverage. That being said, the other pieces of paint armor don't wrap around the edges so they are still noticeable too. One last major problem with the 'factory installed' paint armor (BTW when I saw 'factory-installed' paint armor, its not actually Tesla, but a 3rd party contractor), is that the installs themselves have been pretty shabby jobs. Some people have seen noticeable ripples and other defects.
So that being said, a LOT of people on here (including myself), are opting for aftermarket paint protection. XPEL Ultimate seems to be very popular. This is the cream of the crop, top notch quality, and has 'self-healing' properties. (if it gets scratched, some water and sunlight makes the scratch go away). In addition, *THE EDGES ARE WRAPPED*, so you don't see any lines at all. I actually get my car this Wednesday, and Sunday I have an appt with a local XPEL Ultimate installer. (btw, my installer also said he just got done last week ripping off a factory installed paint armor on a Tesla Model S and putting XPEL Ultimate on because the third-party Tesla job was absolutely terrible with very noticeable ripples...he was shocked at how much of an amateur job was done for a $100k vehicle and was wondering why Tesla doesn't contract with higher quality XPEL Ultimate installers). I am having XPEL Ultimate Full hood, full fenders, mirrors, and bumper armored for $1395. So this is what I would recommend. There are a few threads on here in detail about XPEL Ultimate installs with pictures so search around. I will post my pictures late Sunday.