When a certain module is not needed, it should not cause a problem when any of its dependencies are not in the classpath.
For example, if your not using JPA and therefor no JPA deps are in the classpath, following exception occurs:

java.lang.NoClassDefFoundError: org/springframework/orm/hibernate3/LocalSessionFactoryBean
at org.unitils.orm.hibernate.HibernateModule.createOrmPersistenceUnitLoader(HibernateModule.java:140)
at org.unitils.orm.common.OrmModule.init(OrmModule.java:83)
at org.unitils.orm.hibernate.HibernateModule.init(HibernateModule.java:83)

This should result in a simple warning and the module should be ignored.

For now, you can disable to the modules you don't need as a work-around, by adding the corresponding following properties

unitils.module.database.enabled=false
unitils.module.hibernate.enabled=false
unitils.module.dbunit.enabled=false
unitils.module.mock.enabled=false
unitils.module.easymock.enabled=false
unitils.module.inject.enabled=false
unitils.module.spring.enabled=false
unitils.module.jpa.enabled=false