Good guide, but it can be improved a lot. The coding is neat and the guide doesn't burn my eyes out like some of these newer guides so good job on that :3

• Rune notes contradict the runes (unless you meant a full AP rune page)
• Lich Bane where? :(
• I don't believe Liandry's Torment is core on AP Sona.
• You should probably add alternatives (to runes, items, etc.)
• I believe you take Barrier when you know your enemy is like LeBlanc or something, definitely viable.
• Tough Skin o.o
• You don't really give actual information on laning with Sona, simply warding and zone tips. When you add a section called "Laning Phase" you should probably actually explain how you would play Sona.
  tl;dr for above point - Add more gameplay information.

I didn't get past the item section.

Can't believe you didn't notice the Tough Skin , lol.

Buying rod of ages that late and lacking lick bane is a big -1.

I think you missed out Void Staff and probably Zhonya's Hourglass. If you consider Rod of Ages as an option, whatever, it should be rushed. I don't think that Barrier is such an odd choice.
In your Rune section you used the wrong codings: Greater Glyph of Ability Power and not Glyph of Ability Power.

Excellent guide overall. I personally would run HPen Marks over MPen, but either way works. The standard 9 points in the Defense Mastery Tree would also be Block , Unyielding , Recovery , Veteran Scars and Juggernaut . Enchanted Armor isn't too effective, since you are only building one defensive item. You may want to consider Lich Bane as well. Your finished builds have Greater Totem instead of Greater Vision Totem or Greater Stealth Totem, and you have crecendo instead of Crescendo in your combo section. Anyhow, the guide looks good. Good luck!

By the way, you ought to turn on C2V in your guide settings.