The following options can be set using GERONIMO_OPTS system variable so that the settings could take effect by the time of server startup.
On a Windows: set GERONIMO_OPTS=-D<OptionClass>=<value>
On non-Windows systems: export GERONIMO_OPTS=-D<OptionClass>=<value>

OptionClass:org.apache.geronimo.deployment.LenientMFCP
Value: true, false
Default: false
Description: Specify lenience vs. strict manifest classpath interpretation. Specify "true" for more lenient processing such as ignoring missing jars and references that are not spec compliant.
Found in framework\modules\geronimo-deployment\src\main\java\org\apache\geronimo\deployment\DeploymentContext.java

OptionClass:org.apache.geronimo.deployment.util.DeploymentUtil.jarUrlRewrite
Value: true, false
Default: false
Description: To prevent the lockout of archive during deployment, instead of returning a jar url, write the content to a temp file and return the url of that file.
Found in framework\modules\geronimo-deployment\src\main\java\org\apache\geronimo\deployment\util\DeploymentUtil.java

OptionClass:org.apache.geronimo.gbean.NoProxy
Value: true, false
Default: true
Description: Specify whether to use fast proxy to access GBean. If not, reflection is used.
Found in framework\modules\geronimo-kernel\src\main\java\org\apache\geronimo\gbean\runtime\AbstractGBeanReference.java

OptionClass:org.apache.geronimo.kernel.config.Marshaler
Default: OptionClass:org.apache.geronimo.kernel.config.SerializedConfigurationMarshaler
Description: Specify the configuration marshaler class.
Found in framework\modules\geronimo-kernel\src\main\java\org\apache\geronimo\kernel\config\ConfigurationUtil.java

OptionClass:org.apache.geronimo.kernel.config.MPCLSearchOption
Value: safe, optimized
Default: safe
Description: Specify classLoaderSearchMode of the MultiParentClassLoader
Found in framework\modules\geronimo-kernel\src\main\java\org\apache\geronimo\kernel\config\MultiParentClassLoader.java

geronimo.bootstrap.logging.enabled
Value: true, false
Default: true
Description: TODO
Found in framework\modules\geronimo-kernel\src\main\java\org\apache\geronimo\kernel\log\GeronimoLogging.java

OptionClass:org.apache.geronimo.jacc.policy.provider
Default: Policy provider of the JRE
Description: Specify the classname of the JACC policy provider. Must be a subclass of java.security.Policy.
Found in framework\modules\geronimo-security\src\main\java\org\apache\geronimo\security\jacc\mappingprovider\GeronimoPolicy.java

OptionClass:org.apache.geronimo.config.file
Description: Specify the server config file
Found in framework\modules\geronimo-system\src\main\java\org\apache\geronimo\system\configuration\LocalAttributeManager.java

OptionClass:org.apache.geronimo.config.substitutions.file
Description: Specify the server config substitutions file
Found in framework\modules\geronimo-system\src\main\java\org\apache\geronimo\system\configuration\LocalAttributeManager.java

OptionClass:org.apache.geronimo.config.substitution.prefix
Default: org.apache.geronimo.config.substitution.
Description: Specify the prefix used to specify config substitutions. Users can specify a (key, value) to override the properties set in the config substitutions file. For example, an entry such as hostName=localhost can be overridden by setting OptionClass:org.apache.geronimo.config.substitution.hostName=foo when the prefix is "OptionClass:org.apache.geronimo.config.substitution.".
Found in framework\modules\geronimo-system\src\main\java\org\apache\geronimo\system\configuration\LocalAttributeManager.java

OptionClass:org.apache.geronimo.home.dir
Description: Specify geronimo installation directory
Found in framework\modules\geronimo-system\src\main\java\org\apache\geronimo\system\serverinfo\BasicServerInfo.java

OptionClass:org.apache.geronimo.server.dir
Description: Specify the base dir of a server instance
Found in framework\modules\geronimo-system\src\main\java\org\apache\geronimo\system\serverinfo\BasicServerInfo.java

OptionClass:org.apache.geronimo.server.name
Description: Specify the name of a server instance, used to construct the base dir as a sub-dir of the geronimo installation dir when OptionClass:org.apache.geronimo.server.dir is not specified.
Found in framework\modules\geronimo-system\src\main\java\org\apache\geronimo\system\serverinfo\BasicServerInfo.java

OptionClass:org.apache.geronimo.repository.boot.path
Description: Specify the path of the server repository?
Found in plugins\jaxws\geronimo-jaxws-builder\src\main\java\org\apache\geronimo\jaxws\builder\JAXWSToolsCLI.java

OptionClass:org.apache.geronimo.jaxws.wsgen.addToClassPath
Value: true, false
Default: true
Description: TODO
Found in plugins\jaxws\geronimo-jaxws-builder\src\main\java\org\apache\geronimo\jaxws\builder\WsdlGenerator.java

OptionClass:org.apache.geronimo.jaxws.wsgen.fork
Value: true, false
Default: true on Windows, false on other OS
Description: TODO
Found in plugins\jaxws\geronimo-jaxws-builder\src\main\java\org\apache\geronimo\jaxws\builder\WsdlGenerator.java

OptionClass:org.apache.geronimo.jaxws.wsgen.fork.timeout
Default: 1000 * 60 (microseconds)
Description: TODO
Found in plugins\jaxws\geronimo-jaxws-builder\src\main\java\org\apache\geronimo\jaxws\builder\WsdlGenerator.java

OptionClass:org.apache.geronimo.tomcat.GeronimoStandardContext.allowLinking
Value: true, false
Default: false
Description: TODO
Found in plugins\tomcat\geronimo-tomcat6\src\main\java\org\apache\geronimo\tomcat\GeronimoStandardContext.java

OptionClass:org.apache.geronimo.saaj.provider
Value: axis2, sun
Default: not set.
Description: Specify the SAAJ provider.
Found in plugins\webservices\geronimo-webservices\src\main\java\org\apache\geronimo\webservices\saaj\SAAJFactoryFinder.java

OptionClass:org.apache.geronimo.jaxws.builder.useSimpleFinder
Value: true, false
Default: not set
Description: Use org.apache.geronimo.jaxws.builder.SimpleWARWebServiceFinder to locate WebServiceInfo objects,otherwise use org.apache.geronimo.jaxws.builder.AdvancedWARWebServiceFinder.
Found in plugins/jaxws/geronimo-jaxws-builder/src/main/java/org/apache/geronimo/jaxws/builder/WebServiceFinder