If you've got data sitting in one place and then data sitting in another, it's generally a massive fucking pain in the ass.
Speaking from my experience anyway. Bonus points if one of them was written by a company in the early 2000s who didn't trust those newfangled RDBMSes to get it right. Extra bonus points if they thought UTF-8 was for sissies.
We primarily use MySQL and CouchDB (BigCouch). Our user records (accounts and payment) are stored the RDBMS, while the data the users created is in BigCouch. We enjoy the schemaless nature, durability and scalability of BigCouch a lot.
Depending on your definition of "database system", we also have a hefty Solr index (for search), some Redis (no persistence only to connect systems/services via pubsub) and Memcache (cache).