In my project (similar to mediafire and rapidshare), clients can upload files to the server. I am using DB2 database and IBM WAS
Well my Opinion would be to store the relevant information like path, name, description, etc... in the database and keep the file evtl. encrypted on the filesystem, it would be cheaper to scale your system adding a webserver than adding a database one as webspace is cheap comparing with databases, all you will need then is to add an IP column to your database or server name so you can address teh new webserver.
It's general knowledge that storing files in the database -especially big ones- it's generally a bad idea. There are brilliant explanations in these questions:
Storing a file in a database as opposed to the file system?
Storing Images in DB - Yea or Nay?
And I'd like to highlight some points myself:
There are Pros and Cons for storing BLOBs in the database.
You need to judge for yourself which advantage and which disadvantage is more important for you.
I don't share the wide-spread assumption that storing BLOBs in a database is always a bad idea. It depends - as with many other decisions.