He writes all of the Morning Musume songs except
-Mikaeri Bijin
-Ima Koko Kara
-Imasugu Tobikomu Yuuki
-Utakata Saturday Night
-Mukidashi de Mukiatte
Just to clarify: He was the sound producer for Ima sugu, which was composed by Taisei, his Sharan Q bandmate. Although Mikaeri wasn't written or composed by Tsunku, it was at least produced by him as it was released just before his hiatus (he even handpicked the lyricist). Ima Koko Kara was actually the first MM song without any involvement from Tsunku whatsoever, and it was a cover with an anime tie-up anyway so it's understandable.
The fact that Utakata was such a huge success without Tsunku is an indication of the direction MM will follow from now on. They tried making a MM song without Tsunku, it worked fantastically well, which is probably what got us Mukidashi on the new single. Mukidashi is also really popular among fans. They might experiment with two non-Tsunku a-sides next time instead of just one.
As far as other groups go, the last single Tsunku had complete control over was Juice=Juice/NEXT YOU's Next is you! and it was a one-time deal. It's entirely possible that °C-ute's final single will get special treatment too. He does nothing but a few songs unless specified.
After °C-ute and Momoko graduate, H!P will have more members and groups who were not chosen by Tsunku than the opposite. MM's 12th gen are the last H!P members who were selected before his hiatus and knowing how bad his condition was at the time, he might have not even chosen them himself. Honestly, I only expect his involvement to decrease as "his" girls move on to other things.