What is the best way to learn music theory on your own?

Music theory is a vast topic. Wikipedia is the best place to learn music theory as per my experience. Having someone who can help in guiding you on what to learn next will be a better option in case you are starting new. I started going through Wikipedia and finding it very interesting. Most of the things are mathematics what I feel. As there are lots of scale and all the scales can be played in 12 different keys, things starts to become more complex. I have been using an Android app called Music Companion during the course of my learning and that is helping me a lot in understanding Scales, what chords to play in each scale, Circle of Fifths for each scale etc. It also has a built in metronome with very nice timing and chords can be played along with Metronome beat as accompaniment. You too can try it.

The app is available here: Music Companion - Apps on Google Play

What are the best android apps for learning and understanding music theory?

Music theory is a vast topic which evolved through long period of time and still evolving. There are different varieties of musics practiced throughout the world and that makes the things more complex. Though the theory is complex yet there are many commonalities between them and that helps understanding the theory easily. Wikipedia is a good source of information.

I have found an Android app called Music Companion which helped me a lot in understanding different Scales, Chords to be played in any Scale, formation of Chords, Circle of Fifth(/Fourth) for all the scales etc. It also has a built in Metronome with very good timing and chords can be played along with the Metronome beats.

The app can be found here: Music Companion - Apps on Google Play

Hope this will help other music enthusiasts as well.

What music theory should I learn if I want to know what chords go together on the guitar?

You should learn about Scales, Chords that can be played on different notes of the scale, alternate chords, Circle of fifth etc.

You can use Music Companion - Apps on Google Play Android app that can help you in all these.