PHP and Java are both perfectly suitable for developing web services (although PHP might be easier to get started with), but Intel XDK does not support developing web services.
As far as how to connect your XDK app to web services, the following resources might be useful:
Video: Ajax Requests and REST Based Web Services in the Intel® XDK
Video: Ajax Requests and REST Based Web Services in the Intel® XDK - Part 2
Document: (Integrating Web Services in Intel XDK) Overview
Hope this helps!