Well, ideally, your company should have a coding standards document or something. If they don't, you should go ahead and suggest to your boss that one should be established. At the very least, your company should be using java's coding standards documentation (Code Conventions for the Java Programming Language
You can take the messy approach to refactoring and code cleaning: doing it as you go about your usual tasks. If you need to fix a bug in a section of code, consider gently modifying the surrounding code to meet the java coding standard (things like adding qualifiers, javadocs, and other non-invasive adjustments).
If you notice deprecated methods or classes being used, point them out to a coworker, saying a possible improvement needs to take place there. Just be vigilant on significant issues and try to send them up the chain of commands. You can't do much more than that.