"Workflows" is quite a broad category. There are native legacy workflows which run in our manager service which perform machine state management, external workflow, and provisioning. You're probably referring to distributed workflows that run the DEM's, which can be created in design center. In either case, I don't believe there's a command line interface as part of the product or out in the community to control their execution. CloudUtil is mostly used as a configuration utility for loading and manipulating the installation of the workflows and execution.
There are ways to do this programmatically through the REST interface, but you have to have pretty good knowledge about the execution system since it is essentially similar to manipulating the database. I had written some powershell utilities in the past like this but they're not worth posting in this context.
If I were writing one again, I'd implement it as a C# powershell cmdlet module for use like a powercli. If someone writes it in the community I'd love to use it!!
EDIT: One major challenge with firing workflows from standard console application is that event workflows take complex types as arguments.
