If databases weren't meant to store binary data, why do we have the BLOB column type available? There are strong arguments for and against on both sides of the argument, though often the strongest side tends to be to store the files in the file system and make a reference to the file name and/or path using a simple VARCHAR column.
One of the benefits of using a database system over the file system to store files is to overcome throughput issues.
Having directories of millions of files for example can kill IO throughput. Databases can overcome this because usually they use a single table space. Not to mention they have sophisticated data caching methods.
But do remember, a file system was designed to store files, so in the majority of cases it is advisable to use it.
So the most likely conclusion is to store small types of binary data in the database, like documents and small images, but store files of great size, like say 100MB or maybe 1000MB (1GB) on the filesystem.