Taverna Workbench has an integrated provenance collection facility. As a workflow runs, events are recorded from each service invocation. You can explore intermediate inputs and outputs by clicking on a service on the graph or in the progress table in the Results Perspective. If there is iteration over the service, you can see individual invocations.
The provenance (intermediate values) viewer is useful for evaluating previous workflow runs and also for debugging workflows at the time of design.