I am using Eclipse 3.3.2 with the latest version of the Force.com IDE 13.0.0.200806130415.  If any of the salesforce code is loaded, for example opening the force.com perspective, the help contents will not load anymore.  If I open up Eclipse and make sure that only the java perspective loads then the help contents opens fine.  I have pasted the exceptions that are written to the Eclipse error log below.  Right now the workaround is to close the force.com perspective and any code files that are open prior to closing Eclipse.  Then when Eclipse starts back up no salesforce code is loaded.  You can then launch the help before opening the force.com perspective and code files from your project.

!ENTRY com.salesforce.toolkit 1 0 2008-08-23 09:19:44.098
 !MESSAGE INFO [09:19:44] (ApexCodeEditor.java:doSetInput:222) - Set resource attributes on 'src/unpackaged/classes/clsAssociateMethods.cls'

!ENTRY org.eclipse.ui 4 0 2008-08-23 09:20:53.426
!MESSAGE Unhandled event loop exception
!STACK 0
java.lang.ExceptionInInitializerError at org.eclipse.equinox.http.jetty.internal.HttpServerManager.updated(HttpServerManager.java:78) at org.eclipse.equinox.http.jetty.internal.Activator.startServer(Activator.java:208) at org.eclipse.equinox.http.jetty.JettyConfigurator.startServer(JettyConfigurator.java:60) at org.eclipse.help.internal.server.WebappManager.start(WebappManager.java:43) at org.eclipse.help.internal.base.BaseHelpSystem.ensureWebappRunning(BaseHelpSystem.java:187) at org.eclipse.help.internal.base.HelpDisplay.displayHelpURL(HelpDisplay.java:152) at org.eclipse.help.internal.base.HelpDisplay.displayHelp(HelpDisplay.java:42) at org.eclipse.help.ui.internal.DefaultHelpUI.displayHelp(DefaultHelpUI.java:125) at org.eclipse.ui.internal.help.WorkbenchHelpSystem.displayHelp(WorkbenchHelpSystem.java:833) at org.eclipse.ui.internal.actions.HelpContentsAction$1.run(HelpContentsAction.java:83) at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:67) at org.eclipse.ui.internal.actions.HelpContentsAction.run(HelpContentsAction.java:81) at org.eclipse.jface.action.Action.runWithEvent(Action.java:498) at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:546) at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:490) at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:402) at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:66) at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:938) at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:3682) at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3293) at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2389) at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2353) at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2219) at org.eclipse.ui.internal.Workbench$4.run(Workbench.java:466) at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:289) at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:461) at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149) at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:106) at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:169) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:106) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:76) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:363) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:176) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:508) at org.eclipse.equinox.launcher.Main.basicRun(Main.java:447) at org.eclipse.equinox.launcher.Main.run(Main.java:1173) Caused by: org.apache.commons.logging.LogConfigurationException: org.apache.commons.logging.LogConfigurationException: No suitable Log constructor [Ljava.lang.Class;@deea66 for org.apache.commons.logging.impl.Log4JLogger (Caused by java.lang.NoClassDefFoundError: org/apache/log4j/Category) (Caused by org.apache.commons.logging.LogConfigurationException: No suitable Log constructor [Ljava.lang.Class;@deea66 for org.apache.commons.logging.impl.Log4JLogger (Caused by java.lang.NoClassDefFoundError: org/apache/log4j/Category)) at org.apache.commons.logging.impl.LogFactoryImpl.newInstance(LogFactoryImpl.java:543) at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:235) at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:209) at org.mortbay.log.LogFactory.getLog(LogFactory.java:28) at org.mortbay.util.Container.<clinit>(Container.java:39) ... 40 more Caused by: org.apache.commons.logging.LogConfigurationException: No suitable Log constructor [Ljava.lang.Class;@deea66 for org.apache.commons.logging.impl.Log4JLogger (Caused by java.lang.NoClassDefFoundError: org/apache/log4j/Category) at org.apache.commons.logging.impl.LogFactoryImpl.getLogConstructor(LogFactoryImpl.java:413) at org.apache.commons.logging.impl.LogFactoryImpl.newInstance(LogFactoryImpl.java:529) ... 44 more Caused by: java.lang.NoClassDefFoundError: org/apache/log4j/Category at java.lang.Class.getDeclaredConstructors0(Native Method) at java.lang.Class.privateGetDeclaredConstructors(Unknown Source) at java.lang.Class.getConstructor0(Unknown Source) at java.lang.Class.getConstructor(Unknown Source) at org.apache.commons.logging.impl.LogFactoryImpl.getLogConstructor(LogFactoryImpl.java:410) ... 45 more Caused by: java.lang.ClassNotFoundException: org.apache.log4j.Category at java.lang.ClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at org.eclipse.osgi.framework.internal.core.BundleLoader.findClassInternal(BundleLoader.java:429) at org.eclipse.osgi.framework.internal.core.BundleLoader.findClass(BundleLoader.java:369) at org.eclipse.osgi.framework.internal.core.BundleLoader.findClass(BundleLoader.java:357) at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:83) at java.lang.ClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClassInternal(Unknown Source) ... 50 more

!ENTRY com.salesforce.toolkit 1 0 2008-08-23 09:20:57.035
!MESSAGE INFO [09:20:57] (ToolkitPlugin.java:stop:90) - Stopping com.salesforce.toolkit plugin