What is the best Web App to run on Linux CGI or Stand Alone
Both have advantages and disadvantages.
Easier to start/stop
Easier to use with SSL
Easier to combine with other website content
Both can be load balanced and/or use a reverse proxy. Some reverse proxies support SSL. It’s mainly whats most comfortable for you, and what your host provides. If you have a box that will only run one app ever then standalone makes sense. If you want to run multiple apps you need to run a proxy so they can bind to different ports and the proxy sits on port 80. If you are going to do that you could just as well use Apache (or similar) as your web server + proxy and get the best of both Worlds.