I want to use a Rpi to interface with 3 atmega ics in an embedded system but the pi seems to only have one uart port. I know arduino can emulate a serial connection over two io pins, will this be possible on a pi? I plan on using a headless raspbian setup with a mono c# terminal application.
What you are referring to is called Software Serial, where bytes are bit banged and create the same effect as a serial port.
Using a normal Linux distribution the answer is, No. The reason is because bit banging required real time processing of data, otherwise the data will just be junk.
You can use a multiplexer which is a cheap way to get 4 serial ports but you cannot use all 4 at the same time. You can switch between ports on demand.
You can buy a SC16IS752 that uses I2C - Which means you can add a few of these with real time data flow. It is more complicated since you have to build everything around it your self.
You also buy cheap USB to UART - a USB Hub and add as many as you like