I've seen quite a few stores that sell both one-of-a-kind branding, and not one-of-a-kind. As long as you specify which is which, and you definitely should charge quite a bit more for the ooak(since you can't sell them more then once you have to get your hourly rate out of one sale).
That being said, you could possibly offer to "customize" your pre-mades - such as multiple color choices, and maybe different fonts. This reduces the chance that someone will see something exactly like the one they bought. Limit to six colors and two fonts choices or something like that.
I think pre-mades "packages" of banners, facebook timelines, blogs, etc is a great idea too. And you definitely need to charge more for your ooaks.