We are considering building an addon that will enable you to migrate theme and plugin files. However, we do recommend storing your theme and plugin files in a version control system like git. Then you can easily deploy using one of the many tools that works with version control.
If you have SSH access to your server, you could setup a git-based deployment system allowing you to simply run “git push” to deploy. Other deployment options when you have SSH access include rsync and capistrano. If you only have FTP access, Dandelion is a great tool to use with git.
You may also want to listen to episode 9 of Apply Filters podcast on deployment and check out this great guide describing how WP Migrate DB Pro fits in with version control and deployment.