The MySQL developers run a couple of large databases (millions of rows). At work, we run a couple of complex databases (several dozen tables). I expect that with tuning and decent hardware, the upper limits are in the billions of rows, hundreds of tables, and multi-gigabytes of data.

If this is all one system and if the data belongs in the database, put it there. Keep an eye on performance and profile when you must, but otherwise, you should be okay.