Most of my Initiates have the now-OOP pewter Templar shoulder pads from GW. The right shoulder is the cross and skull, and the left is the cross and laurel/scroll. Unfortunately, these are now hard to find and I have started to run low on these, so I've had to make do.
For my squad-leading Sword Brethren, one shoulder is the cross and skull from the BT Upgrade Sprue, and the other the pewter cross and laurel. For my specialists such as my apothecary, I'm leaning towards going with the specialist marking on the right, and the cross and laurel on the left, even if it may or may not be entirely supported fluff-wise.
As for those pesky heavy weapons shoulder pads, well, they're not fighty enough to get their own scroll, so I'm thinking I'll pick up those Shapeways Templar crosses for those and what remaining pewter cross and skull pads I have.
When I first painted the army, I tried to denote squads by the colour of the shoulder pads, using red/black black/white white/red, etc, but I've since come to the conclusion that I don't much care for the looks, and I think I'll embark on a new crusade to change it and standardise a bit.