(Pardon the odd appearance of this post, but I figured I'd go for straightforward) My author theories:
1) Future Dipper. Supporting evidence: (a) in Dipper's and Mabel's Guide to Mystery and Nonstop Fun, future Dipper and even-further-in-the-future Dipper appear, and (b) in Bill's entry in Book 2 , it says "He's in my wallet" with a drawing of a -12 dollar bill. Dipper is the only person we know of that has a -12 dollar bill (besides Trembley, though by this logic, it could very well be Trembley). (c) Technically, we do not know Dipper's real name, so it could very well start with an F, or some other name that provides a clue/link to the author. As stated in Double Dipper, "Dipper" is a nick-name given to him because of the birthmark on his forehead. Although this could be his name, I am going to take it as the implication that it is not his true name. [Before you ask, the use of a nickname that is not at all related to a person's name is totally valid. I know several people who have a nickname that is not related to their name, and yet they respond to no other name].
2) Future Mabel. Supporting evidence: (a) Future characters is not out of the question and has been mentioned in both the book and in the trailer. In the second trailer for 2x07 , they shrug off the idea of Mabel being the author, but with all of the theories of the viewers being misled, this could be another example, and (b) in the trailers for 2x07, there is a single frame that has a picutre of Grunkle Stan and of Mabel and the phrase "is the author." Assuming it's not Stan, then it may very well be (future) Mabel.
3) Alternate Stan. By this, I mean that something may have happened that caused the author to "become" Stan as we know him now. Supporting evidence: (a) Stan knows about a lot of the weird stuff happening in Gravity Falls, but seems to be missing a few little pieces. If he himself wrote the book, he would have known about the invisible ink. (b) He had the six-fingered glove in the basement, and while talking to himself (also in 2x01) he touched the handprint on the cover of Book 3. The way that this was animated implies some relation or significance between Stan and the book. (c) The shapeshifter said "that six-fingered freak hasn't been himself in 30 years", which may mean that the author is someone we know in the show but, as I said in the previous idea, that the author has had something happen to him/her.
4) Gompers. Who knows? He is present pretty much everywhere. Maybe the author switched bodies with the goat...
5-ish) I say "ish" because this is not for The Author exactly. McGucket as a co-author or accomplace to The Author. Evidence: The laptop found in Into the Bunker says "property of f". McGucket's first name is Fiddleford. Add in the leaked photo, the cipher at the end of The Golf War, and his presence at a lot of the supernatural events, who knows....
UPDATE: Based on the latest preview of 2x07 , it sounds like Dipper says "Old Man McGucket" when exclaiming about who wrote the journals. Then again, never trust a trailer (we all remember the trailer for The Time Traveler's Pig...)