i believe AH used Photoshop for it, much like they used photoshop for almost everything MSPA (aside from flashes)

which version of photoshop hussie used i have no idea but i think any version would work

i also think hussie made a mini-guide to SBAHJ somewhere on their old formspring or maybe tumblr i can't remember you might wanna look through the Unofficial Homestuck Collection (not recommended)