So, I'm looking for the best guitar learning software... I have special interest in music theory, so... Any ideas? So far I've just peeked on jamorama... But I guess I need someone's second opinion...

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Ive been using Guitar Scales Method for the past few weeks. But it hasn't really been long enough yet for me to say how well it works. Thought about using Guitar Speed Trainer as well.
Power Tab/Guitar Pro
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Guitar Pro is an excellent program for somebody wishing to expand on their musical theory, but in particular, use it to their advantage. If you would like to write music, Guitar Pro is an excellent way to go. You may also learn a few things on musical theory in the process - I sure did.

It has it's downsides, however, as you have to pay to use this software without using it illegally. PowerTab which is free, can make a non-suffice substitute though - meaning it isn't as powerful and does not have as many features.
you may want to check out eMedia Guitar Method. They have a beginner program which is just worthless unless it's your first time picking up a guitar, but the more advanced program is pretty good. It teaches you different techniques that eventually all incorporate into a few songs, which definitely helps to put it into perspective.