Personally, I had good results storing binary files in a database. See some technical advice at
Handling huge BLOB fields with DBI and MySQL.
Notice that you don't have to store the file as one whole field, but you can split it into easy-to-manage chunks. That node explains how to store and retrieve files that way.
About using the file system instead of a database, in the same thread there is an exchange of opinions, where both sides are evaluated. In addition to what is stated there, I would say that storing in a database is advisable if you plan to replicate the database to some other machine. Since MySQL has a built-in replication engine, you should consider this fact as well.
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