> I'm trying to get Squeak running headless on an Amazon ec2 system.

Deploying Squeak is basically always the same. I don’t think AWS would change that in any way. 
EC2 is not an operating system. It's just a cradle for whatever OS you choose. [1]
Squeak is only run headless in a Linux server, so you choose a flavour of Linux, say Ubuntu 16.04 LTS. 

> Has anyone done this? 

Why would it be any different than running on any given Linux? 

> If so, what version of Squeak?

Any version you want. Just make sure the vm and the image are compatible. For example:

/usr/local/lib/squeak/3.10-4/squeak -vm-display-null -vm-sound-null Squeak3.10-7159-basic.image&

The “headless” part comes from the flags between the vm and the image name. Reading the Squeak man page would help. 
Also, stick with official releases of Squeak. Ad hoc matching of the vm to the  image has become confusing in the last four years. I could do it, but it’d be pretty tedious. 

Chris 

[1] http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/EC2_GetStarted.html <http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/EC2_GetStarted.html>
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