[yurikaze]

My best mods have been the following:
Michelin Pilot Sport 4S tires. The ride quality, grip, and noise are way better than even the Michelin Pilot Sport 4 tires it came with. I can only imagine the improvements they would add to a standard FRS/BRZ.

Tein Flex A (Hydraulic Bumpstop) coilovers with EDFC Active Pro and GPS.
These coilovers are incredible, and the active suspension setup is fantastic for daily driving. It'll adjust automatically from a luxurious cushiony ride, to immediately dialed in and responsive exactly when you need it. It's the best of both worlds.

Endless SS-Y brake pads. They have better grip and feel than stock, and won't leave brake dust on your wheels. They are also completely silent.

I'm very impressed with how these mods made it not only a much better handling track and touge car, but also how they upped the daily drivability.
It really brings the car as a whole into competing with cars from a much higher price bracket. Granted, some of these are significant investments, but the level of improvement your car will receive will be well worth it.

Bad mods: HKS drop-in filter I bought at Super Autobacs in Odaiba. Turns out the USDM and JDM airboxes are different, and the filter doesn't fit.
Yokohama Advan A048 tires. Worse grip than PS4S's, super loud, and get greasy when heat cycled.