Is there any mod that lets you know if you've already learned an enchantment when you're looking through a treasure chest or a merchant's inventory? I'm using good ol' pen and paper for vanilla but when I upgrade to PC I'm going download the Wintermyst mod which adds 124 new enchants which will be a lot more trouble to keep up with. Something that marks spells as learned would also be nice but I'm mainly interested in an enchantment marker.

There's http://www.nexusmods.com/skyrim/mods/60445/? - it doesn't actually "mark" stuff as such, but you can go through and figure out what you've already learned by what's left to learn.

I don't know about an enchantment marker, but SkyUI marks books you have read in the inventory menus, including spell books.