(Weblog content (i.e. posts, comments, links, etc.) is stored in the database, hence it can't be touched just by uploading the new files.)
Consider those files you modified when you set up and customized your blog: index.php, wp-layout.css and wp-comments.php are ones most have made at least a few changes to, but are there any others you've edited, such as alterations you could have made to the /wp-admin or wp-include files? These are what you need to concern yourself about. But as we don't know what you've edited, we can't provide a list of what not to touch.
It's always a good idea to keep a backup of all your WP files, so that if you update a file but find it included a modifcation you need, you can easily add it back.