Weka isn't limited to the GUI if you want to mine your data. It's a regular JAR file you can drop in your server-side web application and make calls to it like any other Java library. I've used it in some of my apps for some clustering algorithms (the easy stuff, since it can get complicated).

I've also written a few articles on Weka if you want to read a few nice tutorials on how to use it. I'm not a Data Mining Expert, but I've had a few semesters of it in grad school.

http://www.ibm.com/developerworks/opensource/library/os-weka...

https://www.ibm.com/developerworks/opensource/library/os-wek...

https://www.ibm.com/developerworks/opensource/library/os-wek...