Difference between Mega 5v and Due 3.3v?

What is the difference between let's say, The Mega 2560 that works on a 5v logical system and the Due that works on a 3.3v..? Like... What does the voltage affects? Why isn't the Due 5v too?

The difference is the voltage. Every pin puts out that voltage if set to output and HIGH and every pin can only read up to that voltage. The Due is running on 3V3 because the used SAM3X isn't available in a 5V version. You could buy modified versions of the Mega2560 with the option to run them on 3V3 (from other suppliers, not Arduino itself).

There are two main advantages with a 3.3V uC. One is lower power consumption. The second is no need for level converters when interfacing with 3.3V sensors and TFT graphic displays. The downside is if you want to interface with 5V devices or circuits , you need a level converter.

Higher speed processors like the Due can run faster because a transistor switching a smaller voltage range has to move smaller currents and can thus be a smaller transistor.

5V parts can receive a 0/3.3V signal and be happy if they only need 0.6 x Vcc for a high - so 0.6 x 5V = 3V, all good. A 5V part driving into a 3.3V receiver needs to level changed down to 3.3V level to avoid damaging the part - the 5V can overpower the input clamp diodes, possibly blowing them, or feeding thru them and blowing up something else in the chip.
If the signals are slower, a resistor divider can work, if the signals are faster an active component is needed to ensure fast switching times from low to high & high to low. A 74HC4050 powered from 3.3V can do that, other chips powered from 3.3V and with 5V tolerant inputs can be used also - read their datasheet to find out.

That reminds me, the other difference is that anything running at 3.3V is going to be a slower clockspeed that a 5V uC (which can run at 16Mhz)

Ha ha ha, raschemmel, that is pretty funny!

The Arduino Due is a microcontroller board based on the Atmel SAM3X8E ARM Cortex-M3 CPU (datasheet). It is the first Arduino board based on a 32-bit ARM core microcontroller. It has 54 digital input/output pins (of which 12 can be used as PWM outputs), 12 analog inputs, 4 UARTs (hardware serial ports), a 84 MHz clock, an USB OTG capable connection, 2 DAC (digital to analog), 2 TWI, a power jack, an SPI header, a JTAG header, a reset button and an erase button.

84 MHz is > 16 MHz.
Guess what voltage the GHz (Giga Hertz, = 1000 MegaHertz) Atmel or AMD processor in your laptop/desktop runs at? Anything > 3.3V will not be a correct answer.

This is borrow story from other forum.

When the Fab scales down for the next technology, the gate oxide thickness in MOS transistors must also be reduced. The big jump was from 0.5um to 0.35um technologies. This was really the first time when gate oxides were reduced below 10nm. At 10nm, the gate oxide can hold off 8Volts so it can easily be used for 5Volts. Since everyone that made power supplies only guaranteed on +/-10%, that meant the MOS must be reliable at 5.5Volts. Two problems : one is that a 10nm oxide when it gets above 8V it starts to tunnel electrons through it. That is how they can be used in EEPROMs and Flash. But worse than this, at high drain voltages hot electrons are injected into the channel and bulk of the Si. These can implant themselevs into the gate ioxide causing unreversible damage (unlike the tunneling case). So the 10nm oxide also had to withstand hot electrons from drain voltages at 5.5V.
OK so we want to shrink to 0.35um. Unfortunately it is not worth shrinking if you do not shrink vertically as well a laterally. Next best oxide was around 7nm. This starts to tunnel close to 7 volts and cannot withstand hot electrons from 5.5V on the drain. So the fab industry said:
"We want to lower the power supply to below 5V" with a big cheesy smile expecting nothing but complete compliance.
The board industry (in particular PC motherboards) said :
"Not frickin likely - in you dreams !"

So the fab industry got extremely upset at this and went off and engineered around it. Two gate thicknesses, 1 to interface with those really mean board people at 5.5V and one just for the boys. 3.6V was chosen as the max to provide enough for high speed drive capability and good immunity to hot electrons. Since the power supply guys live in the eighteenth century the maintained +/- 10% so 3.3V was chosen as centre 3.0V to 3.6V.

Then one day, a fab with enough muscle went to the board guys and said:
"You go 3.3V or you dont get any pentiums"

The board guys then said
"Stuff you we'll go AMD"

To which the fab guys said
"Only kidding! You can stay 5V"

Then one day another fab guy with muscle said
"3.3V or nae Athlons!"
To which the board guys said
"Oops!"

Then all the boards went to 3.3V. The fab guys feeling really pleased with themselves said "Lets shrink to 0.18um and annoy the hell out of the board guys!"
At 0.18um, gate oxides were reduced to about 3.5nm. This oxide can only stand about 2.5V on the drain for hot electrons. So the fab guys went for 2.0V max about 3-4x the threshold voltage. With +/-10% stuck hard, this meant 1.6V to 2.0V so 1.8V nominal.
And then they all went back to start annoying the board guys again.

The boards are still about 3.3V nominally although some chips are still 5V

Ha ha ha, raschemmel, that is pretty funny!

I guess I wasn't even in the same ball park on that one ! Thanks for clarifying that .

And then they all went back to start annoying the board guys again.

The boards are still about 3.3V nominally although some chips are still 5V

"And everyone lived happily ever after...."

Not really. The fast memory parts are even lower: 1.2V!

See page 23 here for voltage supplied to the Intel Core i7 processor.

The 1.5V or the 1.8V ?

The Arduino Due is a microcontroller board based on the Atmel SAM3X8E ARM Cortex-M3 CPU (datasheet). It is the first Arduino board based on a 32-bit ARM core microcontroller. It has 54 digital input/output pins (of which 12 can be used as PWM outputs), 12 analog inputs, 4 UARTs (hardware serial ports), a 84 MHz clock, an USB OTG capable connection, 2 DAC (digital to analog), 2 TWI, a power jack, an SPI header, a JTAG header, a reset button and an erase button.

That's a lot of bang for 40 bucks