One of the unfortunate things about Meteor at the moment is there aren't many open projects to learn from. For others trying to gain insights to best practices through this projects, here are some suggestions I may offer:

Users.find({last_seen: {$lt: (now - 60 * 1000)}}).forEach(function (user) { Users.remove(user._id); });

-> Users.remove({ last_seen: { $lt: (now - 60 * 1000) } });

and

Messages.find({date: {$gt: new Date()}}).forEach(function (message) { Messages.update(message._id, {$set: {date: new Date()}}); });

-> Messages.update({date: {$gt: new Date()}}, { $set: {+new Date() }})

Excellent work otherwise though. I'd love to see more open source projects released with Meteor if anything for others to learn from!