Use the 5V one for sensors and components that can use or require 5V logic.

Use the 3V one to interface with sensors and devices that need 3V logic, or when you want to power it off of a LiPo battery. Both work the same, but have different operating logic voltages.

You can't stack a big shield on it but for many small & simple projects the Trinket will be your go-to platform. In fact we even made some simple modifications to the Arduino IDE so that it works like a mini-Arduino board. We designed a USB bootloader so you can plug it into any computer and reprogram it over a USB port just like an Arduino. The Attiny85 is a fun processor because despite being so small, it has 8K of flash, and 5 I/O pins, including analog inputs and PWM 'analog' outputs. It's our lowest-cost arduino-IDE programmable board! Perfect for when you don't want to give up your expensive dev-board and you aren't willing to take apart the project you worked so hard to design. We wanted to design a microcontroller board that was small enough to fit into any project, and low cost enough to use without hesitation. Trinket may be small, but do not be fooled by its size! It's a tiny microcontroller board, built around the Atmel ATtiny85, a little chip with a lot of power.

Adafruit trinket 5v keyboard