SteamWorks and Steam Cloud support?

[Dr Bob]

If we use any steamworks stuff it is gonna be very optional!

You could take the route Borderlands took.

All Steam Store purchases of Borderlands include support for Steam achievements; an element of Steamworks.

However, retail purchases of Borderlands include no support for Steam and no achievements - not even in-game achievements a la Mass Effect 2.

That way, Steam-activated and Steam-purchased copies of Amnesia will provide the Steamworks facilities to people who want them, such as achievements, cloud-based syncing for your savegames and leaderboards to name a few.