Fan Game Download Directory

http://dic.nicovideo.jp/a/%E3%82%86%E3%82%81%E3%81%AB%E3%81%A3%E3%81%8D%E6%B4%BE%E7%94%9F
Although its not all the fangames, this does cover some of the most complete and a majority of the ones in the Japanese community, along with a few English ones.

Here are some that aren't included in the link above:
The Other Line v0.05
http://www.mediafire.com/?ctah0z8ih2fsavd

May
http://www.mediafire.com/download.php?uc1c25p578tkpi8

Remedy
http://www.mediafire.com/?json0uwe3ce4igi
(Patch) http://www.mediafire.com/?3ake6267bg2hso7

I will update the download links as the games are updated

Here are a few English Translations:
.flow (Norton users beware, it will be deleted as soon as it finishes downloading so you will want to save it to an SD card or USB then transfer it over to your computer)
http://www.mediafire.com/?u5oxw5vq8sh9koh English Locale version, no changing system locale, comes complete with missing map and vehicle file.

LCD DEM
http://www.mediafire.com/?u5oxw5vq8sh9koh Not an English locale

Yume Nisshi is now v0.02
Uploader: http://loda.jp/zenmaigahara_toxic/

There is also an english Translation for this version
http://www.mediafire.com/?n3mqjw5capejfr7
you can thank FuckYeahYumeNisshi on tumblr for it