one index.php for multiple application

It can probably be done, but you'd need to be able to figure out a way to detect which application is being called and set the appropriate $application path in index.php to point to the correct application.

actually that is the reason I made the question. So far I try to search on google about how to setting the index.php for multiple apps in one CI, but the result is always about make different index.php files and rename them according the apps.

How are you planning on serving up the different applications?

Subdomains?
app1.somesite.com
app2.somesite.com

Urls?
somesite.com/app1/controller
somesite.com/app2/controller

subdomain.