Your selection of the IDE might also be based on what your deployment target is as they support different code types.
Visual COBOL for Visual Studio provides support for development of native Windows applications or those that target the .NET Framework. If you are looking for tools to modernize your application with a GUI front end using Microsoft's Winforms or WPF or to create a Windows web site or WCF Web Service to run under IIS then this would be your best bet.
Visual COBOL for Eclipse provides support for development of native Windows applications or you can compile your applications as Java byte code to be run under a JVM. You can also use VC for Eclipse in conjunction with the Visual COBOL DevHub product to do remote development on Linux/Unix systems.
You might want to take a look at the Product Overview here:
If by COBOL for the mainframe you mean Enterprise Developer, it allows for full mainframe COBOL development on the PC including support for CICS, JCL, IMS, etc. where you can develop and debug your applications as well as run them in the Enterprise Server product on the PC.
For more information on the Enterprise products please look here:
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