Difference between capacitors of same value but different sizes
They will probably have different dielectric, meaning different working temperature and tolerance. See table here: http://en.wikipedia.org/wiki/Ceramic_capacitor#Class_2_ceramic_capacitors

Also, bigger capacitors will usually have higher voltage rating, they cool down better.

It also might be age (caps get smaller with years) or manufacturing capabilities. For example of the latter: if you were to buy strictly "Made in Russia" parts, you'd have to tolerate with much larger packages for the same thing, say, Murata makes.

Sometimes (or even usually) there is no real difference, so you can choose depending on the size itself: if you solder by hand, bigger size can be an advantage.

I also remember reading one interesting app-note, focusing on Capacitance as a function of DC Voltage. Generally, physically smaller caps "degrade" more. You can find it here: http://www.maximintegrated.com/en/app-notes/index.mvp/id/5527