Japanese Subtitles

D-Addicts - Subtitles Index Drama subtitles in multiple languages, including Japanese.
kitsunekko.net Japanese and English subtitles for many Anime.
Anisource.net Jpn.Subs Japanese Subs ~ Full-packs for Raws-4U releases.
JPsubbers Japanese Subtitles Drama subtitles. This is the source for a lot of subtitles that are on D-Addicts, raw from the TV streams, and need to be timed in most cases.
Subs4Movies.com Japanese Japanese subtitles mostly for American shows and movies.
OpenSubtitles Japanese Japanese subtitles mostly for American shows and movies.
日本語字幕 (nihongo-jimaku) Subs for Western movies, mainly American ones. Most subtitles are links from the Subscene and similar websites.

Transcripts

Anime Transcripts@アニメで英語 A volunteer-driven collection of anime transcripts in English and Japanese.
Drama Note@どらま・のーと Scripts of Japanese drama. The site hasn't been updated for a while.

Where do you guys get Japanese subs these days? (2015 February 04)
Japanese subtitles for American shows (2015 January 14)
Scripts of Japanese Shows (2014 September 09)
Where to find Japanese subtitles ? (2014 July 10)
Japanese Subs (2013 September 01)
Japanese drama subtitles (2012 November 26)
Dramas with subs in Japanese (2012 January 10)
Japanese subs (2011 October 26)
Japanese Anime Subtitles (2011 June 15)
Where to get J subs fo popular anime? (2011 June 04)
Media with Japanese subtitles online (2010 August 09)
Where do you get your subtitles for anime (英 + 日) (2010 January 12)
Japanese subtitles (2009 November 10)
Japanese Subtitles for Films (2009 August 10)
Downloading Japanese subtitles (subs only) (2009 May 22)
Place to get Japanese subtitles? (2008 October 05)
Exact Japanese subs for dramas and anime (2008 July 07)