Bigfoot?
In the forest scene of the song, we see a glimpse of a hairy figure. Some believe him to be Bigfoot. Others believe him to be Stan or Soos. Personally, I think he is the author of the journals, seen in Gideon Rises.
whisper
At the end of the music, if you listen closely, you can hear a whisper. In the first 6 episodes, it seems to say "I'm still here". But, backwards, it says "Three letters back". This is how you decode the secret messages in the credits of those episodes.
In the next 7 episodes, the whisper is replaced with one that is gibberish forward, but backwards says "Switch A and Z". Again, use this cipher to decode the messages in these episodes.
In the last 7 episodes of the season, the whisper is again replaced. This one says "Stan's museum" forwards, but "26 letters" backwards. The messages are numbers, joined together by dashes, and can be converted to letters by the code A=1, B=2, C=3, etc.
In Gideon Rises, the third whisper is still there, but it only serves to help you translate the message in the journal during the credits video. It says "Reverse the ciphers." So you use all three ciphers in reverse order to decode that message.
In season 2 thus far, the whisper backwards says "Key vigenere". This cipher uses a keyword to translate the coded message. Think of it as a Caesar cipher for each letter. If the letter used in the keyword is a, then to encode the message you would go 0 letters forward (the message would stay the same.) If the letter is b, you would go 1 letter forward. If the letter is c, you would go 2 letters forward, and so on. So if the "three letters back" cipher used earlier was a key vigenere cipher, the keyword would be dddd. Each letter in the keyword is d, so each letter in the message goes three letters forward when encoded, and three letters back when decoded.
The first letter of the keyword is used to encode the first letter of the message, the second letter is used to encode the second letter, etc. When you get to the end of the keyword, cycle around and use the first letter again. Click the link below if you are still confused.
Also in Season 2, there is an image from one of the journals at the end of each episode. That image is decoded with the three ciphers in reverse, as was the one from Gideon Rises. (A1Z26, to atbash, to Caesar set three letters back.)
This page is a list of cryptograms.
Dipper's Guide to the Unexplained
In Boyz Crazy, Stan mentions subliminal, backwards messages hidden in music. This is an obvious reference to the theme song's whisper.
Shortened version
Northwest Mansion Mystery used a shortened version of the theme song. Alex said that this was done due to time constraints, and will only be repeated for huge episodes.
