Bookmarking a subreddit adds it to your bookmarks list in your subreddit menu.
Bookmarking does not automatically subscribe you to the subreddit. This can be handy for subreddits you wish to visit often, but don't wish to appear on your front page like subscribed subreddits do. You can simply select the bookmark from the menu to see posts in that subreddit at any time.
You can also bookmark subscribed subreddits and use the bookmark for quick access.