I've been exactly where you are.
One trick is, even if you're going to have conditions in code, don't switch on Symbian versions. It makes it difficult to add support for new versions in future, or to customise for handsets which are unusual in some way. Instead, identify what the actual properties are that you're relying on, write the code around those, and then include a header file which does:
#if S60_3rd_ED
#define CAF_AGENT 1
#define HTTP_FILE_UPLOAD 1
#elif S60_2nd_ED
#define CAF_AGENT 0
#if S60_2nd_ED_FP2
#define HTTP_FILE_UPLOAD 1
#else
#define HTTP_FILE_UPLOAD 0
#endif
#endif
and so on. Obviously you can group the defines by feature rather than by version if you prefer, have completely different headers per configuration, or whatever scheme suits you.
We had defines for the UI classes you inherit from, too, so that there was some UI code in common between S60 and UIQ. In fact because of what the product was, we didn't have much UI-related code, so a decent proportion of it was common.
As others say, though, it's even better to herd the variable behaviour into classes and functions where possible, and link different versions.
[Edit in response to comment:
We tried quite hard to avoid doing anything dependent on resolution - fortunately the particular app didn't make this too difficult, so our limited UI was pretty generic. The main thing where we switched on screen resolution was for splash/background images and the like. We had a script to preprocess the build files, which substituted the width and height into a file name, splash_240x320.bmp or whatever. We actually hand-generated the images, since there weren't all that many different sizes and the images didn't change often. The same script generated a .h file containing #defines of most of the values used in the build file generation.
This is for per-device builds: we also had more generic SIS files which just resized images on the fly, but we often had requirements on installed size (ROM was sometimes quite limited, which matters if your app is part of the base device image), and resizing images was one way to keep it down a bit. To support screen rotation on N92, Z8, etc, we still needed portrait and landscape versions of some images, since flipping aspect ratio doesn't give as good results as resizing to the same or similar ratio...]