Can I run an ATmega on 3.3V with an external 16 MHz crystal?
According to the specifications, and probably over the entire temperature range the MCU is rated for, no. 

However, I can say I have unintentionally had projects where I used a 16 MHz crystal with a ATmega328P that was run at 3.3V without any issues I noticed, though this was only ever at room temperature.  Out of curiosity, I also experimented with a ATmega2560, and it also managed 16 MHz at 3.3V without any noticeable issues.

It's important to note that there is a difference between "work in one situation", and "work in all situations the MCU's datasheet rates it for. While in this case, my experiments ran fine, there is no guarantee that this will be true for any other ATmega part, or even the same ATmega part from a different production lot. 

It's also possible that some of the MCU peripherals may not work properly, and I simply didn't test them. In particular, I'd worry about the EEPRON and flash self-programming components to be more sensitive to voltage variance.

If this is for a personal project, you may well be fine, particularly if occasional odd behavior is not a problem. However, if this is a actual commercial product, I'd never be willing to risk running a device outside of the specified operating conditions from the datasheet.