WssRemoveFeatureFromSite is a great tool to have in your SharePoint arsenal.  I combined it with some Windows commands to create a batch file that removes multiple features from a site or sitecollection.  This isn’t real complicated stuff, but most useful things aren’t. set site=http://www.example.com/sites/site set scope=site :: Analytics WssRemoveFeatureFromSite -scope %scope% -url %site% -featureid 56dd7fe7-a155-4283-b5e6-6147560601ee [...]

I used a tool by Steven Van de Craen called FaultyFeatureTool to compare the features that were enabled on two different sites. It’s not the original purpose of this tool but it came in very handy. You can also remove the feature using the application or STSADM. STSADM -o deactivatefeature -id <FEATUREID>-url http://localhost -force