I feel to advance myself as a credible guitar player, I need to learn some music theory. I always get discouraged while jamming or watching videos of people like Vai and Petrucci, and they mention that something is in this time signature or that scale. I just feel like I am missing out, and not knowing anything is really hindering my songwriting attempts.

Do you guys have any suggestions on books I can buy or download, or maybe some websites (I am looking through the UG lessons area) that really start from the beginning?

I feel I should also mention that I want to do this because I have been playing guitar for 5 years and I think I have come as far as I can without knowing jack.

www.musictheory.net is a great site with a lot information. A great place to start learning theory.
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Yeah, justinguitar.com is a great place to start... Also, make sure you start with the most basic stuff and then build on it... Otherwise you'll soon get very, very confused...

Also, I found music theory way, WAY easier to "visualize" on piano, so if you have access to that, I really recommend you try it!

i've just started trying to learn theory and at least for me the "for dummies" book was pretty helpful, but i couldnt even read music so you may be farther ahead than me, but i covers all the basic stuff, time signatures, intervals, scales, chord construction and progression pretty well.