So, I have a 500GB HDD @7200RPM.
It is split as:

C: 97GB

D: 179GB

E: 188GB

My belief is to keep OS ONLY in C:\ and any adamant programs that won't go anywhere apart from C:\ [because this speeds up the PC during startup process] and install programs in D:\ so that in case I have to reinstall the OS, I will have the programs readily available after reinstall.
But I have begun to think this approach is flawed because if C:\ is formatted, I will lose registry values and stuff that goes in %appdata% and so it is no use keeping programs in D:/ drive because they will be useless after all.

Should I go ahead and install ALL of my programs in C:\ and then use D:\ and E:\ for storing my data like photos, text files, java files n all?

How will this impact the performance of the HDD?

I only have 3 programs in D:\Program Files so it will be easy to reinstall them :)