OK so I am just starting to lean about micro controllers for a new project and have run into a block. I need to control 30 switches independently(I am making a clock display). Could I do this on something like the Arduino Prototyping Shield with a breadboard ? Or will I need to make my own board? Anything to point me in the right direction is much appreciated.
You are getting a bit confused, you don't control switches you read them. So do you want to read or control things?
Thirty is no problem you just need some sort of hardware expansion probably your best bet would be to use some shift registers.
See:-
http://www.arduino.cc/en/Tutorial/ShiftIn for extra inputs or :-
http://www.arduino.cc/en/Tutorial/ShiftOut for extra outputs.