Since I mostly write for The Hobbit/Lord of the Rings that is currently the only fandom with its own subcategories, my fics divided by pairing into Gen, Kilbo and Other/Multiple (I also try to note any significant minor pairings that show up in the description, particularly for fics that I still consider gen). And my gender term/translation chart for LotR can be found here.
My other fandoms are mostly lumped together under the same page, though I will separate some of them out as they gain more fics, and crossovers/fusions are posted under their own page in order to keep down the mess. All one-shots are now sorted alphabetically within each section (with chaptered fics and series at the end) and all chaptered fics are linked internally because that's a huge pet peeve of mine.
Finally, you should definitely read any warnings on the fics themselves because I've only marked NSFW and non-con on my masterlists.
THE HOBBIT / LotR:
-Gen (or essentially gen)
-Avengers/Captain America (Primarily Steve/Bucky)
-Bourne (Primarily Jason/Kirill)
-Case Closed (HeiShin)
-the Covenant (Caleb/Chase)
-Ghost Ship (Primarily Munder/Dodge)
-Hemlock Grove (Peter/Roman)
-Kazemakase Tsukikage Ran (Ran/Myao)
-Kings (Primarily David/Jack)
-Leverage (Primarily Eliot/Hardison)
-Mass Effect (Kaidan/MShep)
-Maze Runner (Minho/Thomas)
-Pacific Rim (Primarily Raleigh/Chuck)
-Resident Evil (Leon/Everyone)
-Static Shock (Hotstreak/Static)
-Warcraft (Primarily Anduin/Khadgar)
CROSSOVERS & FUSIONS