Other people had this problem too:
http://dev.eclipse.org/newslists/news.eclipse.newcomer/msg12749.html
But I couldn't find any solutions posted.
I fixed it by patching the JST/JSP plugin that caused the error message (see stack trace below) to include the contents of the servletapi-2.3.jar file. It would have been better to change the classpath for the plugin so it could find that jarfile elsewhere but I didn't know how to do it at the time.
Download link for the patched plugin: http://www.buhacoff.net/2007/projects/eclipse-updatingjspindex/org.eclipse.jst.jsp.core_1.0.1.v2006021502002350.jar
Stack trace:
!ENTRY org.eclipse.core.jobs 4 2 2007-11-07 14:44:46.138
!MESSAGE An internal error occurred during: "Updating JSP Index".
!STACK 0
java.lang.NoClassDefFoundError: javax/servlet/jsp/tagext/TagLibraryInfo
at org.eclipse.jst.jsp.core.internal.taglib.TaglibHelperCache.createNewHelper(TaglibHelperCache.java:112)
at org.eclipse.jst.jsp.core.internal.taglib.TaglibHelperCache.getHelper(TaglibHelperCache.java:97)
at org.eclipse.jst.jsp.core.internal.taglib.TaglibHelperManager.getHelperFromCache(TaglibHelperManager.java:43)
at org.eclipse.jst.jsp.core.internal.taglib.TaglibHelperManager.getTaglibHelper(TaglibHelperManager.java:36)
at org.eclipse.jst.jsp.core.internal.java.JSPTranslator.addTaglibVariables(JSPTranslator.java:684)
at org.eclipse.jst.jsp.core.internal.java.JSPTranslator.translateXMLNode(JSPTranslator.java:997)
at org.eclipse.jst.jsp.core.internal.java.JSPTranslator.translateRegionContainer(JSPTranslator.java:843)
at org.eclipse.jst.jsp.core.internal.java.JSPTranslator.translate(JSPTranslator.java:734)
at org.eclipse.jst.jsp.core.internal.java.JSPTranslationAdapter.getJSPTranslation(JSPTranslationAdapter.java:131)
at org.eclipse.jst.jsp.core.internal.java.search.JSPSearchDocument.getJSPTranslation(JSPSearchDocument.java:112)
at org.eclipse.jst.jsp.core.internal.java.search.JSPSearchDocument.getPath(JSPSearchDocument.java:149)
at org.eclipse.jst.jsp.core.internal.java.search.JavaSearchDocumentDelegate.(JavaSearchDocumentDelegate.java:30)
at org.eclipse.jst.jsp.core.internal.java.search.JSPSearchSupport.createSearchDocument(JSPSearchSupport.java:401)
at org.eclipse.jst.jsp.core.internal.java.search.JSPSearchSupport.addJspFile(JSPSearchSupport.java:295)
at org.eclipse.jst.jsp.core.internal.java.search.JSPIndexManager$ProcessFilesJob.run(JSPIndexManager.java:262)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:58)
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