Cleaning Up a 5V Line Pulling 1 Amp
The simplest thing to do to start with is to add some smoothing caps on the 5V line - a 10uF ceramic and something like a 47uF tantalum would help to keep some of the lower frequency ripple under control.

If you can adjust the voltage of your DC-DC, one option would be to increase the voltage to say 5.3V, and then use a low noise 5V LDO (e.g. TPS7A85) which will help to clean up any switching noise. Setting the DC-DC voltage to just greater than the drop-out voltage of the LDO will help to keep losses and heat generation to a minimum.

Additionally you can look at splitting your supply regions up using feed-through capacitors. These act like L-C filters and have great noise rejection. By placing one between the main power supply rail and sensitive components, you can isolate some of the noise in the system.

Finally for sensitive components, you can add more than one ceramic cap close to the power pins. If you use a series of values in parallel, such as 0.1uF + 10nF + 1nF, with the smallest value closest to the power pins, you will increase the effectiveness of the filtering over a larger range of frequencies.



As an example, we are working on a 12-channel 370MSPS ADC board with ultra low jitter clocks. As it stands that board has 12 amplifiers, 6 ADC ICs and a clock generator. Each one has local power planes, separated from the main power planes using feed-through capacitors to isolate noise. We have ended up with 43 power regions, supplied by 12 LDOs which are in turn supplied by 7 DC-DC regulators. On that board there are over 600 capacitors alone! 

The one thing we have done on this board is to not split up the ground planes. There is a nice application note (I'll see if I can find the link) which explains how actually splitting up the ground plane can cause more issues than it solves from a noise perspective. The key thing is to keep an eye on the placement of components - for example keeping noisy things like switching regulators away from sensitive analogue circuitry. By keeping an eye on when the current return paths will be, you can keep noise contained even on one single ground plane.