3 Pin Addressable LED's
These are primarily the WS2811, WS2812, WS2812B or NeoPixel series of LED's.
These are inexpensive compared to 4 pin strips.
You can use several pins to drive multiple strips with them.
The disadvantage is that FastLED disables interrupts, so you can't use libraries that rely on interrupts (such as IR remote) at the same time on an 8 bit AVR.
4 Pin Addressable LED's
These are primarily WS2801, LPD8806, APA102 or DotStar series of LED's.
The advantage of these is that FastLED doesn't disable interrupts, so you can use 3rd party libraries that require interrupts.
In addition, these LED strips support a much higher refresh rate and can be used in POV applications.
FastLED doesn't support multiple strips though.