Use interfaces to define your classes. Having an interface means that you can have multiple implementations of the same interface, one for each of the clients. This will require you to analyze your existing codebase and identify logical separations in your code where these interfaces can be defined.
You then have the ability to load an interface as needed based on the client. You could, for example, do this via configuration. Based on a configuration value you load Implementation1 or Implementation2. There are many, many ways to accomplish this particular bit. You should read up on dependency injection, inversion of control and have a look at tools like Ninject, Autofac, Unity.
It may actually be difficult at first considering how you have been using preprocessor directives but seeing as how your application is growing, you will need this refactoring to happen. Keep in mind that if you do not do it now, this refactoring will be a lot more expensive later as your application becomes more complex.