Currently, you are able to gain 125% of the initial value of the given science.  Each time you perform science, you reduce the value you will receive in the future.  Regardless of how you acquire it, you will always end up maxing out at 125% the initial value for a particular area and method of doing science.  It doesn't matter if you transmit your science or return it to Kerbin.

Now, there is good reason for choosing transmission over return, or vice versa.  Early in the career, you don't have access to RTG's, solar panels, or even batteries.  This makes transmitting science impractical at best, as you need electricity from your engines in order to transmit again, so you need to return your science.  Conversely, if you're sending a robotic mission to Jool, it's impractical return a dozen Science Jr. pods and Mystery Goo containers if you want to gather science from as many of the moons as possible.  You're better off sticking a bunch of solar panels on it and transmitting often.

Basically, if the cost (in terms of electricity) isn't too high to transmit _and_ you're able to reacquire the same science easily, transmit it, but always hold on to the last bit of science you have if you're returning the craft to Kerbin.