You have two options:
- You have a a Web server and know how to program a server-side application, in PHP, Python, Java or whatever language is allowed by your ISP;
- You don't have this luxury...
In the first case, you can write an application that get the high scores of the players and store them, ready to re-display them, perhaps with comparison with the other players (top 10, top 50 or whatever). If the server is the one that provides the applet, no need to sign the jar.
In the second case, you have to sign the applet (that might discourage some users), and to ask the user where to store the score file (you can use System.getProperty("user.home") to get a relatively system independent location, but I discourage that as it ends up "spamming" this top folder).
Ah, actually, as you suggested you can have a third option (never tried it): communicate with some JavaScript on the page your applet is, and ask it to set a cookie.