"You've got the choice of writing an 8051 file system or a PC application to read data in whatever non-file system format you choose."

The OP didn't mention a PC at all, although it's a pretty reasonable assumption that the data will eventually wind up on one. It seems to me that the simplest approach, however, is to store data on whatever storage device is chosen in it's native format - bytes, sectors, whatever. Transfer the data to the PC or whatever via the serial port - I realise this is pretty slow but in a data logger application this might not be important. 1 minute 40 seconds per megabyte or thereabouts should be achievable at 115200 baud.

Implementing a filesystem is almost bound to be more difficult than implementing a custom storage solution tailored to the type of data and type of storage device.

Choosing whether or not to use a filesystem is a bit like the OS or no OS debate - in my opinion (and experience) it's best not to unless there are compelling reasons to do so.