Check out the Will/Rachel and Matt/Lea post on gleeclub from a few months ago , most of my favorite fics were recommended by the people there.
Now, some personal favorites:
“The Map is Not The Territory” . That fic is probably the ultimate Will/Rachel fic out there. I’ve seen people who don’t ship it sigh at the reading of this fic. Seriously well written and in character and non-creepy at all. Amazing.
My favorite future! fic (not finished yet) is Chances by 0penhearts.
(That’s the link to the last chapter, but the links for the rest are there)
By milk_and_glass:
Ordinary Thursdays
I Like It Clandestine
By tattooedsiren Climb a Ladder to the Stars
The City is for Strangers by youcallitwinter
And finally Nothing Thrills Us (It was never finished, and it needed a beta, but it was really good story-wise)
Those are all that come to mind. You can always go to glee_kink_meme on Livejournal and check out the filled prompts too but they’re usually not my cup of tea (except “Columbus”, that fic is amazing and there’s a link to it on the Will/Rachel gleeclub post)