I mean doujin in the sense of a fanwork based on an established franchise not doujin as in amatuer.
There’s two that I know of that make these on a regular basis. Of the two I like Crimson better for their artwork and because they put voice acting in their games:
- Crimson Comics (there’s also its subgroup Dancing Queen but they haven’t released anything in years)
http://www.alles.or.jp/~uir/index1.htm
- Saberfish:
Anything with the ??(???) tag on EGS would be an example. This (free samples here) is probably the most unusual example I’ve come across, although Itsumono Tokoro’s works aren’t too far behind.
Itsumono Tokoro has made a heap of doujin (all-ages) titles, many of which are free now. ONF (parody of ONE) and Kanoso (parody of Kanon) are great reads.
On DLsite and at events like Comiket you’ll also find plenty of low quality nukige based on established franchises, typically whatever is popular at the moment (so while Oreimo was showing there were a number of Oreimo eroges released etc.) In this regard they’re similar to doujin manga.