I have several applications that are/have been developed using the same tools/technologies (Maven, Java, Subversion, etc.) and properties (such as the same code formatting rules).
Each application consists of multiple projects (on average ~4). Should all projects reside in one Eclipse IDE workspace or should separate workspaces be created for each application?
I usually work within separate projects within the same workspace. If the technologies are similar I find myself more productive if I don't have to re-create the whole workspace. Even if there are multiple applications with several projects, clear naming of projects keeps things organized. For my needs the project options are sufficient for my different environments. Multiple workspaces are more useful to me when I'm developing with different platforms. (Java vs Python)
The truth is it comes down to personal preference. Eclipse is such a versatile tool, and there are just as many ways to use it as there are ways to configure it. Finding something that works for you is probably the best solution.