PECL/ECL Logic

I am trying to integrate an optical transceiver on an Arduino UNO and the transceiver uses PECL (which is similar to ECL +5 V). Here is what it looks like (the bottom trace) http://www.ni.com/cms/images/devzone/tut/a/07c0be30313.gif.

Where would I start with this? Just a simple loop making one pin HIGH and one pin LOW and then delaying it and swapping the pins?

It is a differential output, you only need to use one of the signals, that's all.

As you say , PECL, is Positive referenced ECL

ECL is what you might consider up side down,
a '1' in ECL is about -1v , and a '0' in ECL is about -2 volts.

This was done for noise reasons, as the ground is normally lower noise than the 'other' supply,

PECL changed this, so '1' is about 4 volts, '0' is about 3 volts .....

please check the data sheet of the source as to what you have.

PECL is normally used in devices that are expecting to be 'fast' , so surprising to see in an opto sencor.
if its driving over any distance, its best to use a PECL to TTL translator chip,
such as these http://www.onsemi.com/PowerSolutions/product.do?id=MC100ELT21

You can get away with circuits, such as if you are only detecting a change, then a capacitor can be used in series to generate a TTL spike the arduino can see,

What sort of speed you lookign at ?

Here is the transceiver we currently have:

(if the link doesn't work it is an Avago AFBR-5803TZ transceiver)

It is a relatively cheap transceiver that can go up to speeds of 100 Mb/s using PECL. I am not looking to max the data rate, so kb/s is fine also.

looks to me like you have a digital output that is

High is : Vcc - 1.085 to Vcc -0.88

Low is : Vcc - 1.83 to Vcc - 1.55

Cheep and slow, stuff this into the analog input on the Arduino,

else,
get a converter chip,

If you are not familar with ECL be careful ECL logic is very particular.
With the ECL load resistors are not included in the integrated circuit you have to add it, is mandatory..
Also if you use it at fréquency above few MHz you have to use line impedance matched 50 ohm.

If you are not familar with ECL the best is you read documentation as:
http://ece.wpi.edu/analog/resources/and8020-d.pdf

ON (formerly Motorola) is a major actor in ECL technologie

Please notice that output current in ECL is often 20 mA per Output.