I’m working on an application for a Nursing students; It is a program where a user enters data about their Patient’s Vitals, Skin Assessments, Medicine Administered, etc.
Flowchart for program structure in respect to Data:

That data needs to be saved in a structure divisible by Patient and then by the Time recorded. Problem is this is going to be a HUGE amount of data since entries need to be made every 15 minutes.
Flowchart for what interactions necessary between the project and its data:

request patient var over Time and request populate timeline both search for all entries of that patient between two given dates.
The best way I can think of how to organize this data is directory based:
data/PatientName/Month/19102012.file (the date 19 Oct 2012, for quick omission of ignored dates)
This way might be okay but it feels really hacked together, what better organization should I use for this data?
I honestly don’t think students entering patient data every 15 minutes qualifies as HUGE these days. As such, virtually any technology would be of use. Some sort of relational database is an obvious choice, and given the above, I don’t think you need anything remotely enterprise-scale.
One question that springs to mind is, is security important ? This is medical data, after all. That may influence the technology you choose since filesystems implement security in a radically different fashion to (say) the filesystem.
The one piece of advice I can give now is to abstract your data storage away from the rest of your solution. That way you can implement something trivial now and replace it easily in the future as your requirements solidify.