I See Dead People... In Mirrors
Some of my personal favourites are Trickster and Stars Apart by Willow Rosenberg. They're about the marauders era and are an extremly good read. Trickster won a QSQ for Best Canon Romance and Stars Apart is the sequel to it. James/Lily is the main storyline but it isnt the only one theres also plenty of Sirius, Remus and Peter to go around
Cubicle Conversations with Myrtle
A really good historical fic I've read is called Challah and Pumpkin Juice. It's about a Jewish girl from Vienna coming to Hogwarts to escape the looming threat of WWII, and very very good.
I'm trying to think of others, because I'm very much interested in non-Trio-centric fics. I will certainly second Jess' fics and anything Carole - in specific, she has a good Lavender/Blaise fic set during the Carrows' reign at Hogwarts called Lavender, Blue, and she's also working on a fic about Dean that I'm really interested in called Dean Thomas and the Reiver Curse. P ussycat123 is also excellent; her Marauder fics are usually fun and worth a read.
Looking at my favorites page, I can find a few more.
Neil/Northumbrian is great with Post Hogwarts fics and minor characters. Some really great non-Trio-centric ones (though they're mostly oneshots with one short chaptered...) are Bare, Moon, Summer of '97 and M.I.T.: Muggle Interface Team. Speaking as someone who's not really into Trio-centric stuff, his Grave Days is also really good despite being Trio-centric.
Hearthlinks by Grace Has Victory is Trio era but...very different. Its MC is Sally-Anne Perks, someone who I think is only canon by being named in a Sorting, and is (sort of?) a retelling of Cinderella.
Seven Thousand Sunsets by FullOfLife is a Next Gen starring Rose Weasley. It's dark - there's a really terrible disease involved - but very very good. Also, you may want to click just to find out how Rose being in love with (and working with) Severus Snape can possibly work - that's why I clicked, anyway. xD
Lastly, I have Uncle Fred Calls Him Dick by MagEd. It's next Gen story but it's either AU or ignores DH or something such that Harry's kids are...I think not quite old enough for Hogwarts and he's not in the picture, and Ginny's getting ready to marry some guy who no one really likes but her. Of course, the kids have something to say about that. And stuff happens. It's been a while since I read it but it was really good and I loved her portrayal of the Weasley clan.
EDIT: How in the world did I leave Potter's Pentagon off the list? If you haven't read it, you really really should. Have a link to Schmergo's author page. It's a series of three long fics, about an AU (well technically written pre-DH) next gen, and Schmergo did a great job of building a world of vibrant characters, new and old. They're probably my favorite Next Gen fics, and it's not even the canon Next Gen kids. xD Oh - and if you're craving more of the Pentagon and co. after you finish the trilogy, Schmergo's got a WIP fic going called Pride and Pre-Juiced Plums that's set after they finish at Hogwarts.