A Meteor app does not, by default, add any X-Powered-By headers to HTTP responses, as you might find in various PHP apps. The headers look like:
$ curl -I https://atmosphere.meteor.com HTTP/1.1 200 OK content-type: text/html; charset=utf-8 date: Tue, 31 Dec 2013 23:12:25 GMT connection: keep-alive
However, this doesn't mask that Meteor was used. Viewing the source of a Meteor app will look very distinctive.
<script type="text/javascript"> __meteor_runtime_config__ = {"meteorRelease":"0.6.3.1","ROOT_URL":"http://atmosphere.meteor.com","serverId":"62a4cf6a-3b28-f7b1-418f-3ddf038f84af","DDP_DEFAULT_CONNECTION_URL":"ddp+sockjs://ddp--****-atmosphere.meteor.com/sockjs"}; </script>
If you're trying to avoid people being able to tell you are using Meteor even by viewing source, I don't think that's possible.