FPGA-DAC PCB Design

You may start a religion war on the analog/digital plane separation by bringing this issue ;)

The inportant thing when you have digital and analog parts on the board is that they don't share power or signal lines. The power lines include of course the voltage supply, but also the return currents in the ground plane. One way to ensure that (and the easiest way) is to use separate ground planes. Another way is component placement. With the latter method you need to regroup the digital and analog parts on designated areas, but you still need to be careful with the return currents. If you place the digital part between the analog one and the power supply, you can end up with ground noise.

My personal experience is that you get better EMC by using a single ground plane for everything. Having two planes can increase the risk of having voltage differences between the two planes at some frequencies, causing signal integrity and EMC problems. Whith a carefully designed board you won't have more ground noise that with two planes, but if you work with "old school" routers or designers, it can be difficult to convince them ;)

As for the PLL power supply, I think having a separate ground plane is overkill. Altera doesn't even do that on their development kits IIRC. Just keep in mind to put proper filters and decoupling on the PLL supply pins to avoid noise problems with the rest of the 2.5V supply rail.