<p>We're in the process of developing a measurement device that will be running 
CE 6.0 with CF 3.5 on x86 embedded hardware, a PC is used to control the 
device and is connected with it using ethernet.</p>

<p>We would like to communicate using interfaces (using DCOM (we know it is not 
supported by default on CE6), .NET Remoting or Web services) instead of 
using some sort of (custom) protocol. Calling methods defined in an 
interface is so much easier and elegant then parsing raw data.</p>

<p>What would be the best solution in this case?</p>

I've had some experience setting up comms between CE devices and a PC, and have used custom interfaces using winsock (thwacking some bytes back and forwards) and have tried SOAP. In Windows CE 5.0, the Microsoft provided SOAP server took our device down somehow every couple of hours or so. I spent many weeks trying to work out what was wrong, thinking it was something I'd done wrong. So, I prefer to stick to winsock now because at least I've got a chance of knowing what's going on and can fix it.
Also, CE devices aren't always the quickest performers depending on what hardware you've got. Web-services take up some overhead and time converting data to XML, and this may be a performance hit you are or are not able to afford.