The most deployed database these days is probably SQLite if you count semi-embedded contexts (ie. mobile apps). Excluding that it does look like MySQL is still on top, but Postgres is catching up fast. I completely forgot InnoDB uses clustered indices by default. Regardless, I was referring to most by implementations, not deployment numbers.
Clustering indexes make a lot of sense for many workloads, you just have to design your data model with them in mind.