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Yahoo Pipes is primarily a cloud hosted intelligent content aggregator.
Warewolf, on the other hand, is a self hosted visual service bus, that you can use to rapidly design and implement complex process based solutions with zero coding.

What Warewolf can do that Yahoo pipes can't is give you full control of the data service that you expose.

You can use Warewolf to manipulate the data as you see fit before you exposing it as a service - meaning less client side development for your mobile apps.

You could also monitor the data, store it, mail it, aggregate it, manipulate it, or feed another service with it. These are just a few of the obvious possibilities.