Docker is a popular tool for containerizing applications, allowing developers to package and ship their software efficiently. To containerize a Java application, one needs to have Docker installed and choose a suitable base image, such as Alpine Linux for its small size or the OpenJDK image for compatibility. The process involves compiling the project, selecting a base image, and executing runnable jar files within the container. Logging within containers is simplified by writing logs to standard output, which can be accessed using Docker's logging commands. Configuration management in containers requires careful handling, often utilizing environment variables and Docker volumes for mounting configuration files, adhering to the twelve-factor app methodology. For more complex setups, configuration key/value stores like Consul or etcd can facilitate service discovery, especially when running multiple instances on a single host.