There are several different possibilities. Initially, unless you need the result straight away you need to think about whether you need to process the results straight ahead or whether it is something done later on.
If it is the later, the easiest might be saving it into a database (like MySQL) and then reading said database (either using the Database Toolkit though I have never used that myself, using a Java or .NET method or exporting it to Excel) and then evaluating your data.
If however you need to process the input straight away things get a little bit more complex: You will need to have a server with MATLAB running (or the compiled version of your MATLAB program) and you will need to connect to your PHP (or a similar scripting language) web interface via TCP. Last time I have done it I have used a custom written Java class for this. If you need any pointers I recommend reading this:
(In general undocumentedmatlab.com is one of the best MALTAB websites in my opinion, excluding mathworks.com obviously).If you get stuck let me know and I can try to answer more specific questions. But this should give you a good starting basis. Hope I could help you!
