"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.

"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