Some determining factors might be:
Do you want to let the users select more than one value for a parameter?
Multi-value parameters are only available on the Stored Process server.
Do you want to create streaming output results?
Streaming results are only available on the Stored Process server.
However, there are other, security-based considerations that you might want to consider -- if you want each session started up based on a single-user's id -- this may lead you to choose the Workspace server.
In either case, reading the documentation may help you pin down the other differences. By default, EG picks the Stored Process Server, when you use the EG Stored Process Wizard to create a stored process.