Q:

3V Arduino options

I have an Arduino Mega board to test 3V devices.  Which is the simplest way to connect those 3V devices to the Arduino Mega (it works at 5V) without burning them?  I saw the Adafruit Trinket works at 3V, could be an option?  Since I need many input/outputs (around 50), Arduino Mega is the most suitable in terms of input/outputs pins.  
What do you suggest me to do? 

A:

There are plenty of non-Arduno boards that both give you more power and 3.3V operation.   Personally I love the chipKIT boards (the Max32 is the chipKIT equivalent to the Mega2560). 
If you want to stick with Arduino then consider the Due, which is the same footprint as the Mega2560 but again with more power and 3.3V operation. 
For interfacing 3.3V devices to a 5V board, though, that can be done simply with level shifters.   You need to get the right type though:

Basic GPIO, SPI and UART etc can be done with a simple MOSFET shifter (cheaply available on eBay)
I2C requires a special I2C level shifter (I use the PCA9306) which maintains the open-drain and bidirectional operation required for I2C

