see following Open Source workflow  Engines that are written in Java:

Enhydra Shark Shark is completely based on standards from WfMC and OMG using XPDL as its native workflow definition format. Storage of processes and activities is done using Enhydra DODS.
Codehaus Werkflow Werkflow is a flexible, extensible process- and state-based workflow engine. It aims to satisfy a myriad of possible workflow scenarios, from enterprise-scale business processes to small-scale user-interaction processes. Using a pluggable and layered architecture, workflows with varying semantics can easily be accomodated.
OpenSymphony OSWorkflow What makes OSWorkflow different is that it is extremely flexible.
jBpm jBpm is a flexible, extensible workflow management system. Business processes , expressed in a simple and powerfull language and packaged in process archives, serve as input for the jBpm runtime server. jBpm combines easy  development of workflow-applications with excellent enterprise application integration (EAI) capabilities. jBpm includes a web-application and a scheduler. jBpm is a scalable J2EE application.
wfmOpen WfMOpen is a J2EE based implementation of a workflow facility (workflow engine) as proposed by the Workflow Management Coalition (WfMC) and the Object Management Group (OMG). Workflows are specified using WfMC's XML Process Definition Language (XPDL) with some extensions.
OFBiz Workflow engine  The Open for Business Workflow Engine is based on the WfMC and OMG spec. OFBiz Workflow Engine uses XPDL as its process definition language.
ObjectWeb Bonita Bonita is a flexible cooperative workflow system, compliant to WfMC specifications. A comprehensive set of integrated graphical tools for performing different kind of actions such as process conception, definition, instanciation, control of processes, and interaction with the users and external applications. 100% browser-based environment with Web Services integration that uses SOAP and XML Data binding technologies in order to encapsulate existing workflow business methods and publish them as a J2EE-based web services. A Third Generation Worflow engine based in the activity anticipation model.
Bigbross Bossa The engine is very fast and lightweight, uses a very expressive Petri net notation to define workflows, does not requires a RDBMS and is very simple to use and to integrate with java applications. Actually, it was designed to be embedded.
Taverna The Taverna project aims to provide a language and software tools to facilitate easy use of workflow and distributed compute technology within the eScience community. Taverna is both a workflow enactor and also an editing suite.
JFolder JFolder (formerly PowerFolder) contains features critical to many applications - including web pages, workflow, security, persistence, email, file management, and data access.
Open Business Engine Open Business Engine is an open source  Java workflow engine which supports the Workflow Management Coalition's (WfMC) workflow specifications, including interface 1, also known as XPDL, interface 2/3 known as WAPI and interface 5 for auditing. OBE provides an environment for executing activities in a controlled, centralized environment. OBE supports both synchronous and asynchronous execution of workflows. The primary OBE implementation is based on J2EE.
OpenWFE OpenWFE is an open source java workflow engine. It features 3 components, easily scalable : an engine, a worklist and a web interface. Its workflow definition language is inspired of Scheme, a Lisp dialect, though it is expressed in XML.
Freefluo - Freefluo is a workflow orchestration tool for web services. It can handle WSDL based web service invocation. It supports two XML workflow languages, one based on IBM's WSFL and another named XScufl. Freefluo is very flexible, at its core is a reusable orchestration framework that is not tied to any workflow language or execution architecture. Freefluo includes extension libraries that enable execution of workflows written in a subset of WSFL.
ZBuilder - ZBuilder3 is a second generation of workflow development and management system which intends to be an open source product. It defines a set of standard JMX management interfaces for different workflow engines and their workflows.
Micro-Workflow - The micro-workflow framework targets developers who want to separate the control and logic aspects in their programs, thus making them flow independent. A well-factored flow independent application facilitates change because the most frequent business changes translate into process changes, thus leaving the code intact. Flow independence also fosters reuse, because domain objects make fewer assumptions about the control context in which they operate
con:cern - con:cern is a workflow engine based on an extended case handling approach. A process is described as a set of activities with pre- and postconditions. An activity is executed when its preconditions are met. It manipulates the process item, thereby creating postconditions. The process flow is determined at run-time. This approach is superior to the conventional process flow approach.
Twister - Twister's aim is to provide a new generation, easily integrable, B2B oriented workflow solution in Java, based on the latest specification efforts in this field. The process engine is based on the BPEL business process specifications and Web Services standards.
YAWL - YAWL (Yet Another Workflow Language), an open source workflow language/management system, is based on a rigorous analysis of existing workflow management systems and workflow languages. Unlike traditional systems it provides direct support for most of the workflow patterns (http://www.workflowpatterns.com). YAWL supports the control-flow perspective, the data perspective, and is able to interact with web services declared in WSDL. It is based on a distributed, web-friendly infrastructure.
Zebra - Zebra is a workflow engine - originally developed to fill in the gaps in some commercial and open source workflow engines. The key differences between it and other workflow systems are able to model all the workflows described in workflow patterns, a GUI designer and Hibernate persistence layer.
ActiveBPEL - ActiveBPEL engine is a robust runtime environment that is capable of executing process definitions created to the Business Process Execution Language for Web Services (BPEL4WS, or just BPEL) 1.1 specifications.
XFlow2 - Inspired by simple workflow definition language in XFlow developed to improve its implementation. Externalized SQL in iBatis mapping files. Works as embedded workflow engine.
Apache Agila - A simple business process management (BPM) product that can be easily embedded in other applications and run on a range of devices, including handheld computers.
Antflow - AntFlow is a tool for the automation and scheduiling of data system tasks, including those with complex dependencies and workflow logic. Antflow represents a new approach to simplifying system automation that leverages pipelines of hot folders chained together to perform a given task. Using XML, Antflow associates an automated task, such as data transfer, compression, or encryption, with a directory on the local system. Whenever a file is copied or written into the hot folder, the associated task is executed and the file is moved to the next hot folder in the pipeline for further processing.
MidOffice BPEL Engine - MidOffice BPEL Editor (MOBE) is an open-source platform for process orchestration which executes, monitors, adjusts and terminates pre-defined processes). The platform is implemented using J2EE technologies and standards like BPEL, XML and SOAP.