in my experience having truly separate AGND and DGND nets almost never works out well in practice. 90% of the designs i see that try to do this end up with current loops that introduce EMI issues and can generate more noise in the analog portions of the circuit than using a single ground with careful part placement would.
Having two GND planes also creates a problem for routing in that signals referenced to a particular ground should only ever be run on layers that are adjacent to this plane or its associate power plane. This can result is a pretty funky stack up that can limit where you can run traces. Your best answer would be AGND,signal,?GND,POWER,signal,DGND but thats funky to layout, uses lots of vias, only gives 2 signal layers to route on.
What i would recommend is a single solid ground plane and careful part placement. High speed digital signals and noise will follow the path of least inductance to ground not the path of least resistance. The path of least inductance is the smallest loop area, for signals this is directly under the trace on the adjacent ground plane. In some cases a ground pour on top, bottom, or both can be helpful in reducing noise pick up as well. This is dependent on the components and the design layout.
Create virtual partitions, keep out areas, where you only run either analog or digital signals, keeping in mind that the return current path for the low frequency analog signals is the path of least resistance, while the return path for the high speed digital signals is the path of least inductance. As long as your careful to ensure that the return current paths don't cross, especially a digital return running under your analog sections. You shouldn't get much noise pick up at all.
If your have a particular device that is very sensitive to noise, such as a high resolution ADC, you can use a ground island to increase noise immunity, like this:
alt text http://www.hottconsultants.com/techtips/a-d%20gnd%20plane.gif
In cases where i have some sensitive analog circuitry i will usually also use a power island that is separated from the digital power supply by an LC filter of some sort, depending on the digital frequencies i'm wishing to block.
Do you have any unplated holes or slots in the PCB's? I've previously specified some unplated holes on a similar layer stack, and found that the supposedly unplated holes were in fact plated and the plating was creating a short between the power and ground planes. A round file and a few minutes work quickly sorted the problem out.
Best Answer
Four-layer design with power and ground planes is refreshingly easy compared to two-layer! You'll want to familiarize yourself with the stackup editor in your tool, first off -- as to layer stackup selection, the "canonical", if nothing else because it's the simplest to lay out, stackup for a four layer board is signal - power - ground - signal, assuming your board runs at a single voltage.
When laying out, the signal traces stick to the two signal layers, and power and ground are accessed simply by dropping vias down where appropriate instead of having to run traces for them -- the lack of traces for power and ground running all over the board makes routing far easier. (Even though it's not great for signal integrity, even the most basic of four-layer stackups is still much better than a two-layer board.)