"Wanderings with Werewolves" by ishandtwofourths, and "Caring For Magical Creatures" by MrsTater

These are... sister fics, if you will. They look a lot alike, but one looks a bit more like their grandmother, while the other clearly favors their dear Aunt Prudence.

http://www.fanfiction.net/s/4458074/1/Wanderings_with_werewolves

http://www.fanfiction.net/s/3448191/1/

Lupin/Tonks meet during Lupin's run at Defense professor. Tonks is trying to solve a case, and Lupin is helping. I actually prefer "Wandering with Werewolves," but MrsTater is clearly the superior writer. I don't know. They're Charlotte and Emily Bronte.

"Marauder Reminders" by Jenulus

This is an unfinished Lupin/Tonks fic that, to me, portrays their relationship in the most canon-honest way.

http://www.fanfiction.net/s/2257981/1/Marauder_Reminders#

I think it was Jenulus's original intention to cover their whole courtship, but she only managed to get nine chapters in, so she covers their first meeting at Grimmauld Place and their growing friendship/flirtation.

I just really like the way she portrays these characters. Tonks, in particular, is wonderful, as she is a bit gruffer in this fic than most others.

I'm breaking another one of my rules by posting a piece that's unfinished, but who cares. This had a really, really good start, and it's worth looking into.

"Harry Potter and the Slytherin Spy" by Christine Morgan

What if there was another Hogwarts student in Little Whinging?

This fic, written/set right after Order of the Phoenix, is about Harry meeting a Slytherin girl and forming a friendship with her in his sixth year. It's fairly-straightforward and not excessively (wonderfully) violent at all. (Sarcasm.)

http://www.eskimo.com/~vecna/hp_spy_01.html

Morgan can imitate Rowling's writing style well, and there is something so satisfying about reading a fic you can confuse for the genuine article; especially when it gets to where Morgan is describing gruesome deaths in Rowling's simple, yet descriptive prose.

I'm not pretending this fic is without problems; it's focused on a female OC, which is a no-no to most in the fandom, though trust me when I say the writing is good enough you won't care. And there are a few canon things that would raise eyebrows - Kreacher's characterisation is all wrong in this fic, in my opinion, while I think Morgan's explanation of where Sirius was hiding during Harry's thirteenth summer is a brilliant twist. Morgan also abuses ellipses, and the ending seems a bit rushed and simplistic, but trust me when I say:
YOU SHOULD READ THIS.

"Alexandrite" by Pandora Culpa

Pandora Culpa wrote the book on the Lupin/Tonks pairing. You should check it out sometime.

http://www.fanfiction.net/s/2225991/1/Alexandrite