UPDATE
For newer versions of Meteor you need to remove the mongo package. The mongo package is embedded in the meteor-platform package. So you need to remove that and add all the rest back (from https://github.com/meteor/meteor/tree/devel/packages/meteor-platform):
meteor remove meteor-platform
meteor add meteor webapp logging tracker session ddp blaze spacebars templating check underscore jquery random ejson templating check underscore jquery random ejson
Then your app won't use Mongo anymore :).
In dev mode you can get rid of mongo by setting the MONGO_URL environment variable to something else and start meteor. For example: MONGO_URL=mongodb://nowhere meteor