There are several sites that helped me with learning guitar, that are free of charge! Some include:
www.musictheory.net, this site helps with learning theory, notes on the fretboard, as well as ear training!
www.good-ear.com, this site is a very useful site for ear training, from identifying types of chords, to intervals, to scales, a very good recommended resource for developing the ear.
www.all-guitar-chords.com/, this site can identify just about any chord or scale to plkay on the guitar.
www.ultimate-guitar.com, this site has loads of lessons for beginners, as well as tabs to easily learn your favourite songs.
www.blackbeltguitar.com, this site has many lessons devoted from everything from proper practising techniques, to scales, and even to very experienced guitar techniques and theory.
I hope these resources help. Just keep in mind that these sites are devoted to different areas of learning the guitar so you will have to search around and learn from a few rather than just one site. Youtube is also another good source for learning guitar but keep in mind that some videos may have innaccurate information that could create bad habits. Also be aware of this when browsing other websites. Good luck and have fun with playing guitar!