For my own reference when browsing eBay and the like, I used to keep a list of old albums and singles that had tracks not available on US iTunes. However, it wasn't really applicable to the modern day when everything was made available--at least until Tsunku stopped writing the majority of H!P songs and things stopped being so simple. So here is a list of what's easily missed from 2016. More or less in order of release.
Karada Dake ga Otona ni Nattan ja nai. Available on Next is you! / Karada Dake ga Otona ni Nattan ja nai and Petit Best 17.
Otona no Jijou. Released as a digital single in Japan, it's also on Petit Best 17.
All 4 tracks of Tsubaki Factory SOUND + VISION Vol.1.
H!P-adjacent, all 7 tracks of ONDAS.
Ora wa Ninkimono. Available on Samba! Kobushi Janeiro / Bacchikoi Seishun! / Ora wa Ninkimono and Kobushi Sono Ichi.
Namida no Request. Available on Dou Datte Ii no / Namida no Request.
The 7 cover tracks on the second disc of Kobushi Sono Ichi Limited Edition B.