There are no real differences between RCP and Eclipse IDE applications, except maybe a reduced set of plug-ins to rely on (but they can be brought back). What you might have to take extra care is branding (and theming), and packaging (possible via products). Some RCP tutorials to start with:
In case of RAP, the difference is bigger, as you have to manage the different sessions of different users, and theming is more important. A tutorial for the RAP-based issues (including tips for single sourcing RCP and RAP applications) are available from eclipsesource.com.
A final note: if you are starting a brand new project, I'd rather experiment a bit with the 4.x API, as it is simpler to manage between RCP and RAP.