Just so you know, it isn't Harry/Luna by any means and the relationship develops more in the second part. But just as well I think it's a good story to read. Mind you this has abuse!Harry, fatherly!Snape and well, the typical Severitus fic. The first part pretty much just works on the relationship between Harry and Snape although you'll see Luna's appearance near the end. The second part - The Poor of God has plenty of Luna and H/L friendship-relationship-etc. The latest chapter is a bit worrisome. ;_; Poor Luna.

Title: The Guiltless
Author: kilara25
Rating: T
Other Pairings:
Summary: Sixth year AU, written pre HBP. When Harry appears at the Welcoming Feast wearing a glamor only Snape notices, Snape decides to find out what the glamor is hiding. His investigation leads to a number of shocking revelations about both Harry and himself.
Warnings: Like I mentioned, abused!Harry and angst. If you don't like Snape or pretty much a Severitus fic. This really isn't for you.

Link: http://www.fanfiction.net/s/3621897/1/The_Guiltless

Title: The Poor of God
Author: kilara25
Rating: T
Other Pairings:
Summary: After Snape's visit to Surrey, Harry writes him a thank you letter that triggers an extended correspondence between the two of them.
Warnings: The same. Lots of Luna though and lots of fatherly!Snape towards Luna and Harry. This is where Luna's role is greatly expanded and Harry and Luna becomes a lot closer here more than ever (more because of circumstances but I don't think either of them mind at all, hehe)

Link: http://www.fanfiction.net/s/3744964/1/The_Poor_of_God

I really like the story. The author kinda grips you emotionally IMO. She has another fic where Harry is a girl AU and it's really well done. I recommend it as well.

Luna is my favourite character but next to her? It definitely is Severus Snape. Now that is a kind of character with far too much issues and very gray and I love him all the more for it.