my.ini configuration for a huge server

I have developed a web based app in PHP MySQL and Flash Builder. It was running fine until a few days ago when the client began to connect a lot of users. Then the app started to freeze and sent errors like the back files don't exists any more. When the users started to disconnect the app ran normally again.

I suposse that the problem is the configuration of my.ini. I am not an expert in the variables of this file and I want to get the best performance of the data base in the server. The server is huge and has 32GB RAM, Windows Server 2012 Standard, 100GB in HD, two processor Intel Xeon 2.5 GHZ.

The question is if you can help me with the my.ini variables values according to my app and server hardware. Apologies for my basic English grammar.