Can you explain more about what's contained in these files? How regular is their size and structure, both internal and external? All of these are factors that influence your decision of file system versus database.
in reply to Re^3: Perl solution for storage of large number of small files
in thread Perl solution for storage of large number of small files
I'm just saying that "Millions of small fragments of data" is a vote for database over file system. Answers to the other three questions (regularity of size, internal structure, and external structure) might vote in favor of the file system.