As evanperryg mentioned there are multiple ways of connecting the LEDs to the arduino.
If you only want to turn a few LEDs on and off, then wiring them directly to an arduino is the easiest way to go. Unfortunately it's the most labor intensive as far as wiring goes. THe down side being that you'll need 1 output pin on the arduino per LED unless you design some interfacing electronics to go with it.
If you want multicolor with lots of different patterns then you're going to want to use an LED strip which is talked to over a serial protocol (like I2C for example). THis is the easiers option in my oppinion, especialyl since there are already libraries which handle the majority of the software. Wiring is simple, just 3 wires to conenct between the strip and the arduino.
Edit: I link to this in the other thread, but if you do go this route, there are plenty of good code examples for arduino alread.
I've described how to wire everything up in another
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I can't help you on writing Java or C programs for it, though. I just use whatever language that is in the Arduino software (95% sure it's called Sketch).
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The arduino programming language is based on C/C++. Sketches are what the project/program files are referred to.