Alrighty - so here goes.
The fans I have are brushless, and do require a nice smooth DC voltage to keep the onboard circuitry happy. A simple one-pole low-pass filter can help get this for me. As a first-order approximation, I wanted a filter with a cutoff frequency on or around 20Hz, as when I started, I believed that the RAMPS was doing a 20KHz PWM (Later thinking says that it isn't), and with a three-decade frequency difference, I'd expect a nice 50-60 dB reduction in signal, dropping any amplitude variation by about 500 or so. This would reduce a 6VDC + 6VAC signal (0-12V) to having only a 12mV voltage variation on top of the DC - pretty reasonable. Cutoff frequency is just 1/(2 * Pi * R* C), so RC needs to be on the order of 7.9E-3 ohm*farads.
The eventual goal, at full power, would be to drive a pair of 1.5 Watt fans, so at 12V (full voltage) I'd need 0.25A. Since all current has to go through the resistor in the low pass filter (hereafter LPF), power dissipation in the LPF will be I^2 * R = 0.0625 * R. For any reasonably 'high' value of R, that can be a pain. I don't want to dissipate more than 1W in my LPF, and frankly, would rather dissipate 0.5W so that I can use nice simple resistors. That leads me to a max of 8 Ohms, and a 1 milliFarad capacitor.
Then I realized that this isn't a traditional AC signal. The RAMBO schematics show that the fan is always connected to 12V, and the low-terminal is occasionally connected to ground via the PWM-driven NFET. Thus, it's essentially open-collector, and traditional AC math doesn't quite cut it. In particular, without the driver pulling down as well as up, the technical DC signal is something /like/ 12V anyway. Thus, the concern is that the system is only ever pulled one way, so you don't get a nice average like you'd hope for with a square wave. Instead, the voltage across the cap only gets pulled up by the driver, and only pulled down by the fan.
Setting up a steady-state KCL, at the capacitor, i_Rfilter = i_Fan
i_Rfilter = percent_on * (12 - V_fan)/R_filter
i_Fan = V_fan/R_fan
Setting the two equal, I eventually find...
V_fan = 12 * percent * R_fan / (R_filter + percent * R_fan)
R_fan is approximately 48 Ohms (assuming it's linear, which I'm not sure of, but it'll do), and assuming R_filter is 8 Ohms (from above)...

What we see is that the 8 Ohm resistor in the LPF does reduce the maximum potential of the fans, which can no longer see 12V, even in the best case. More interestingly, the relationship between voltage at the fans and the duty cycle is nonlinear by a large margin. Finally, we note that power dissipated in the LPF is higher than we might have realized at first glance - while the current at high duty cycles does give the fairly low power dissipation we were hoping for, at lower duty cycles there's more of a voltage drop across the filter, leading to higher currents rushing through it, struggling to keep that cap charged. Thus, the 8 Ohm resistor burns what I consider to be too much power.
Resolving the system, then, for various values of filter resistor doesn't really help that much - I keep getting dissipation peaks on the order of 0.8 Watts.

Going with a higher resistor, then, has two benefits:
1) It pushes the exponential farther to the right, looking more and more linear.
2) To get the time constant needed (8 ms), you can use ever-smaller capacitors, and since 1mF caps are fairly large, that's helpful.
The downsides, then, are:
1) General power dissipation. While peaks are near 0.8W for many to most configurations, higher resistor values reach them more often, and more consistently.
2) Peak voltage. Since larger filter resistors essentially make a voltage divider with the load, your peak voltage drops off for the fan. Luckily, most fans work equally well (or too well) at 12V anyway, so this isn't a huge issue.
Currently, I've got a 1 Ohm 5W resistor with a 4mF cap on my system, and my fans do nice things, but due to the non-linearity between duty cycle and fan voltage, my fans turn on at only a 6% duty cycle, and hit near-max flow at only 35% duty cycle. Thus, I set my slic3r fan min to 6%, and max to 35%, giving me the closest to linear I can get.
If I were to buy components again, I'd likely go with a 20 Ohm 5 Watt resistor, and a 400uF cap. Much smaller, and it would likely give me better linearity, and I won't miss the top end of the fans, which I'm not using anyway.

Does anyone see anything I missed? Anything I flubbed up like a bad person? Either way, I hope it at least kept your interest...