I can go along with several others on here and recommend Justin Sandercoe, http://www.justinguitar.com/. Not only does he have a very good free to use learning structure from beginner to intermediate levels, but you can also buy the full course and song books that go along with the beginners course at very reasonable prices (if you would prefer learn that way). This is what Brian May of Queen had to say about Justin.
On a day when there's a temptation to go into a dark place, and only see all the bad stuff there is in the world ... greed, cruelty, exploitation, selfishness ... I get days like that pretty often .... it's great to find someone giving out, and giving out good, and operating on an honour basis ... There are so many people who can't afford Guitar lessons .... well, here's a wonderful guy who has set up a whole system of teaching guitar ... Blues, Jazz, Rock, even Songwriting, from the basics, tuning the guitar, etc ... upwards ... If you use his site, it's up to you to determine how much you can contribute ... but this is an amazing site .... he is also very aware of issues in the world which need attention ... a great channel .. Check him out. He's a giver..
One of the best on the Web as far as I am Concerned.