Supernatural
Accidental Incest - Incest without knowing they are related
Adam Milligan - Fics with him as a main character
Monster AU - AU fics where Sam is being hunted (usually by Dean) for being a psychic/monster.
Outsiders - Fics involving outsiders having the wrong idea about Sam & Dean & thinking they are evil serial killers. Includes crossovers & canon universe fics.
Sam/Dean Rape, Noncon & Dubcon
Sea creatures - Fics where a character is a sea creature like a merman (includes Supernatural RPF fics as well)
Outside links
SD Recs - Sam/Dean thematic recs. Lots of great lists including Amnesia and Prison fics.
Changing Channels Meme - List of TV Land based crossover fics
SPN Nightcrawler - Supernatural and J2 fics involving supernatural creatures such as vampires and shapeshifters (but excluding angels and demons)
SPN Little Bro - Hurt!Sam & hurt!Jensen fic lists organised by type of hurt. Also has a delicious archive.
SPN Remakes - Movie remake fics with Supernatural characters or Supernatural Actors
SPN Story Finders - Good place to ask people for fics based on a trope or theme
SPN Themed Recs - Long-running (since 2006) community that recs fics based on a theme
Suicidal!Sam - Collection of fics where Sam is suicidal/attempts suicide
Suicidal!Sam +character death - Fics where Sam commits suicide and succeeds
Supernatural Fic Recs - A collection of themed rec lists, mostly Sam/Dean relationship related or kinky themes.
Bookmark collections
Chellexxx1 - A collection of more than 8,000 Supernatural and Supernatural RPF fics, mostly Sam/Dean or gen, no mpreg or a/b/o fics.
Redfoxrose (katsheswims) - A collection of more than 2,000 Supernatural fics, as well 3,000 links for fics from other fandoms.
ifyouweremine - 2400+ Supernatural bookmarks, mostly gen or Sam/Dean. Warns for top/bottom dynamics. No links more recent than Feb 2011.
Oh Sam - More than 2000 links of Sam-centric hurt/comfort fics. No links more recent than April 2014.
somersault1509 - 3700+ SPN and SPN RPF fics, all meticulously tagged with tropes, kinks, word count etc.