This is a very old thread, and things have changed a bit. NI-SCOPE now includes the NI-HWS toolset, designed for high performance disk access. It is the successor to the sfpFile API mentioned above. Look at the NI-SCOPE example
niScope EX Save to File - HWS Low Level - Single Channel Stream.vi for how to use it. There are several NI-SCOPE HWS examples for your use. You can find them with the example finder (in LabVIEW
Help->Find Examples...).
An alternate is to use the TDM binary format. I am not experienced it it's use, so can't offer too many hints.
As to which to use, that depends on where your data is going. If you plan to analyze using DIAdem or Excel, use TDM (there is an Excel plug-in). If you plan to analyze using anything else, use HWS. HWS is based on HDF5, so can be read by most analysis packages using the HDF5 tools. If your analysis package does not support HDF5, use raw binary. Anything will read that, but it is not very self-describing.