It seems that the latest developer version of Chrome (7.0.517.0) adds an option to auto-run plugins that are sandboxed, and prompt for the others.
It can be enabled by The Tools menu, then "Preferences", "Under the hood", "Content settings". In "Plug-ins", you can select "Allow only sandboxed plug-ins"
Then, embedded objects that require a plug-in to run will be replaced with a button. There's also an infobar that lets you enable the plug-in for the whole page.
