1. I made the site. There are no viruses.
2. Some of the game systems here can store the games in your temporary files. Most of the game systems do
not store the games on your computer. When you close the game, it is gone forever until you play it again. It is done this way because some of the companies that own the copyrights on these old games get upset when people download full copies of their old games.
3. Disabling Java Temporary files would mean that you would have to download the emulator every time you play a game. If you have broadband that will mean you have to wait a few extra seconds for each game. If you are on dial up then you will have to wait a minute or two extra for each game.
4. Disabling Java Temporary files will have not affect the quality of the games. Only the download speed.
5. Java is a very secure system. I do not think any viruses or other nuisances have ever spread through Java Applets. Java Applets are different from JavaScript which can cause problems in some cases.
6. The exception to the rule above is if the Java Applet pops up a security warning and asks if you "trust this publisher". If you say yes then the Java Applet will be given extra security privileges and theoretically could do something bad. The Text games -
http://www.retrouprising.com/Text.php - on this site have that type of security warning. It is necessary to allow the text games to use save states. Nothing bad will happen if you use save states in our Text games but you have to take my word on that one. Nothing bad
CAN happen in the other Java games. Java is very secure unless you tell it that you "trust this publisher".
7. So there is not much of a benefit if you disable Java Temp File Storage. But unless you are on Dial-Up there isn't much of a negative to disabling it either.
8. You should always have an antivirus program running. I highly recommend installing these free programs.
http://free.grisoft.com/
http://www.safer-networking.org/
http://www.javacoolsoftware.com/spywareblaster.html
http://www.mozilla.com/en-US/firefo
And install all updates from
http://www.update.microsoft.com
9. That covers this site and security. It is possible for some negative things to happen because of Java. Mainly. Your web browser could crash causing you to have to restart it - easy but can be annoying. After you close a game you might still hear the game music. If you do hear music it will stop if you close all open web browser windows and wait 5 seconds. Your computer might run slow. Again close web browser and problem will go away. There is nothing bad that could happen that rebooting would not fix.
10 Happy gaming. Enjoy your stay.
'Cause I don't want to have strange files on the computer I'm using, to keep from getting viruses. Is that an issue? Is Kong there? Would he know? 
(He built the site and gathered the roms; he would know if there are viruses in 'em.) :P
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