1Password 3.8 (from our website) and 1Password 3.9 (from the Mac App Store) are essentially identical. The very slight differences are pretty much just related to application sandboxing which, again, shouldn't make any practical difference in daily use.
We do have a detailed list of the specific changes, though, if you are interested in the geeky details.
I don't think I can stress it enough that there really isn't enough of a difference to make any appreciable difference. Purchase wherever works best for you.
Additionally, if, for some reason, you need to use 1Password 3.8 after purchasing 1Password 3.9 on the Mac App Store, you can email us your MAS receipt and we can create a 3.8 license key for you. The reverse is not possible since Apple doesn't allow any developer to transfer a license into the App Store, so in that regard you may get more flexibility from purchasing on the Mac App Store.