Have a look at this older question: How to: Easily Move a WordPress Install from Development to Production?. It covers migration and deployment of WP installations.
For your more immediate issue, do backups of your database. Use a backup plugin (WP-DB-Backup is what I use, find it on the WP plugins repository) to handle this for you. You needn’t worry as much about the core WP files as those can be loaded up again. You do need to keep backups of your theme files.
Also take a look at this article: http://www.noeltock.com/web-design/wordpress/fast-furious-wordpress-theme-development-pt1/. It’s about using source control to simplify deployments. It’s something I want to give a try!
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