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Seems like this would be a very easy way to DoS a Meteor app, if it's really spawning a PhantomJS process for each request.

It is. And the server doesn't even feed PhantomJS the HTML that it can generate, PhantomJS has to make another request to the server. I wonder if it can be made to recurse? https://github.com/meteor/meteor/blob/master/packages/spider...

If this content is mostly for spiders, I don't see why you couldn't cache the resulting HTML for 1 hour or so and only regenerate new pages.