According to: http://wiki.apache.org/tomcat/UsingPhp php5.x isn't supported.

I managed to get PHP5 running on Tomcat 6. Can I still get support for getting Piwik running in this case?

Opening piwik.php now results in the following message:

Warning: parse_ini_file(config/config.ini.php) [function.parse-ini-file]: failed to open stream: No such file or directory in C:\apache-tomcat-6.0.16\webapps\forphp\core\Tracker\Config.php on line 54
Piwik is a free open source web analytics alternative to Google analytics.

Opening index.php shows the following:

Undefined index: SCRIPT_NAME
in 'C:\apache-tomcat-6.0.16\webapps\forphp\core\Url.php' at the line 89

#0 Piwik_ErrorHandler(8, Undefined index: SCRIPT_NAME, C:\apache-tomcat-6.0.16\webapps\forphp\core\Url.php, 89, Array ([=> )) called at C:\apache-tomcat-6.0.16\webapps\forphp\core\Url.php:89
#1 Piwik_Url::getCurrentScriptName() called at [C:\apache-tomcat-6.0.16\webapps\forphp\core\Url.php:50]
#2 Piwik_Url::getCurrentUrlWithoutFileName() called at [C:\apache-tomcat-6.0.16\webapps\forphp\core\View.php:48]
#3 Piwik_View->__construct(Installation/templates/structure.tpl) called at [C:\apache-tomcat-6.0.16\webapps\forphp\plugins\Installation\View.php:22]
#4 Piwik_Install_View->__construct(Installation/templates/welcome.tpl, Array ([=> welcome,1 => systemCheck,[=> databaseSetup,3 => tablesCreation,[=> generalSetup,5 => firstWebsiteSetup,[=> displayJavascriptCode,7 => finished), welcome) called at [C:\apache-tomcat-6.0.16\webapps\forphp\plugins\Installation\Controller.php:63]
#5 Piwik_Installation_Controller->welcome() called at [C:\apache-tomcat-6.0.16\webapps\forphp\plugins\Installation\Installation.php:61]
#6 Piwik_Installation->startInstallation(Piwik_Event_Notification Object ([=> FrontController.NoConfigurationFile,_notificationObject => Exception Object ([=> The configuration file C:\apache-tomcat-6.0.16\webapps\forphp/config/config.ini.php has not been found., => ,[=> 0, => C:\apache-tomcat-6.0.16\webapps\forphp\core\Config.php,[=> 108, => Array ([=> Array (file => C:\apache-tomcat-6.0.16\webapps\forphp\core\Piwik.php,[=> 1260,function => init,[=> Piwik_Config,type => ->,[=> Array ()),1 => Array ([=> C:\apache-tomcat-6.0.16\webapps\forphp\core\FrontController.php,line => 216,[=> createConfigObject,class => Piwik,[=> ::,args => Array ()),[=> Array (file => C:\apache-tomcat-6.0.16\webapps\forphp\index.php,[=> 48,function => init,[=> Piwik_FrontController,type => ->,[=> Array ()))),_notificationInfo => Array (),[=> 0,_notificationCount => 0))
#7 call_user_func_array(Array ([=> Piwik_Installation Object ( => Piwik_Installation_Controller),[=> startInstallation), Array (0 => Piwik_Event_Notification Object ([=> FrontController.NoConfigurationFile,_notificationObject => Exception Object ([=> The configuration file C:\apache-tomcat-6.0.16\webapps\forphp/config/config.ini.php has not been found., => ,[=> 0, => C:\apache-tomcat-6.0.16\webapps\forphp\core\Config.php,[=> 108, => Array ([=> Array (file => C:\apache-tomcat-6.0.16\webapps\forphp\core\Piwik.php,[=> 1260,function => init,[=> Piwik_Config,type => ->,[=> Array ()),1 => Array ([=> C:\apache-tomcat-6.0.16\webapps\forphp\core\FrontController.php,line => 216,[=> createConfigObject,class => Piwik,[=> ::,args => Array ()),[=> Array (file => C:\apache-tomcat-6.0.16\webapps\forphp\index.php,[=> 48,function => init,[=> Piwik_FrontController,type => ->,[=> Array ()))),_notificationInfo => Array (),[=> 0,_notificationCount => 0))) called at [C:\apache-tomcat-6.0.16\webapps\forphp\libs\Event\Dispatcher.php:214]
#8 Event_Dispatcher->addObserver(Array ([=> Piwik_Installation Object ( => Piwik_Installation_Controller),[=> startInstallation), FrontController.NoConfigurationFile) called at C:\apache-tomcat-6.0.16\webapps\forphp\core\PluginsManager.php:360
#9 Piwik_PluginsManager->addPluginObservers(Piwik_Installation Object ([=> Piwik_Installation_Controller)) called at C:\apache-tomcat-6.0.16\webapps\forphp\core\PluginsManager.php:246
#10 Piwik_PluginsManager->loadPlugins() called at [C:\apache-tomcat-6.0.16\webapps\forphp\core\PluginsManager.php:161]
#11 Piwik_PluginsManager->setPluginsToLoad(Array ([=> CorePluginsAdmin,1 => CoreAdminHome,[=> CoreHome,3 => API,[=> Widgetize,5 => LanguagesManager,[=> Actions,7 => Dashboard,[=> Referers,9 => UserSettings,[=> UserCountry,11 => VisitsSummary,[=> VisitFrequency,13 => VisitTime,[=> VisitorInterest,15 => ExampleAPI,[=> ExamplePlugin,17 => ExampleRssWidget,[=> ExampleFeedburner,19 => ExampleRssWidget,[=> Provider,21 => Feedback,[=> Login,23 => UsersManager,[=> SitesManager,25 => Installation)) called at [C:\apache-tomcat-6.0.16\webapps\forphp\core\FrontController.php:224]
#12 Piwik_FrontController->init() called at [C:\apache-tomcat-6.0.16\webapps\forphp\index.php:48]

Unfortunately, Tomcat doesn't appear to set the SCRIPT_NAME variable; Apache and IIS do, and pass this to PHP. I'll see if there's a workaround, but the problem here lies in Tomcat.

Instead of invoking php-cgi directly, I suggest you have Tomcat run a bash script (wrapper) that sets the missing CGI environment variables and then running the php-cgi executable.