I myself don't like the hot deployment option, mostly for production environments. It is way too easy - which can be convenient sometimes, but it makes it much easier to make mistakes during long overnight deployments. But that is just my personal feeling about it.
Well, I believe there isn't any "standard" way to do that, without some additional paid tool. Remember that you must not only transfer the applications themselves, you have to copy all the resources they use (datasources, queues, etc...).