Currently i am developing administrator system for MySQL.
I am thinking of using JSP to MySQL instead of the famous PHP-MySQL
Can i use the normal Apache server or do i have use Tomcat instead>?
You will need to use Tomcat or some other servlet container to run your JSPs in. Tomcat integrates very well with Apache, so if you're running on a sever that's already using Apache you're fine.
JSPs are nice, but they have some deficiencies when it comes to easily building a web application (PHP has these same problems). JSP are good for the presentation layer, but not the control layer. Many people use Struts in addition to JSP. Personally I use Apache Cocoon which I find to be the best web app framework out there. It's based around XML/XSLT and Java. Ic can run JSP and PHP internally as well as many other components.