What is the best way to make a web service that can be used by Taverna?

Taverna can use many kinds of service, so there are many ways of producing services.

If you are a biologist/bioinformatician with many legacy command-line applications and you want to wrap them as web services, we recommend Soaplab

Soaplab is based on Perl. If you have more experience with Java, you might want to create services using Apache axis. Please see the Axis user guide for more details.