I have recently been trying to nudge the OP in the direction of databases, and that's a nudge I see reflected in many of the responses.

Indeed. I asked a similar question.

Why are you settled upon a "flat file database" rather than one of the other options? (RDBMS, HADOOP, NoSQL etc.)

That said, RDBMSs are pretty shite at handling hierarchal datasets, whereas file-systems are explicitly designed and tuned for exactly that. It would be an interesting exercise to compare the response times for the two using identical, threaded datasets. But then again, neither scale well.

Facebook apparently use hundreds of sharded MySQL instances ensconced behind 1000s of memcache instances with more (PHP!?!) caching in front of that. They seem to make it work, but it sounds like a disaster waiting to happen to me. But we can probably assume that the OP isn't likely to be requiring that scale of things anytime soon.

One nice thing about using the file-system is that it is relatively easy to scale it out across multiple boxes, by partitioning the ID space to pretty much whatever level is required. Raided disks in each box take care of your hardware redundancy and each box trickles off updates in the background to remote off-line storage. Far easier to partition and manage than distributed RDBMSs and no coherency problems.