Real world examples of 3D WSNs are underwater surveillance networks, structural health monitoring of multi-storey buildings, and mountain surface deployment.
Read the following papers for more details.
1) Luo, Jun, Feng Li, and Ying He. "3DQS: Distributed data access in 3D wireless sensor networks." Communications (ICC), 2011 IEEE International Conference on. IEEE, 2011.
2) Nauman Aslam, Optimizing Coverage in 3D Wireless Sensor Networks, Online: www.intechopen.com/download/pdf/12451
3) Miao, Chunyu, et al. "3D Self-Deployment Algorithm in Mobile Wireless Sensor Networks." International Journal of Distributed Sensor Networks 2015 (2015). Online: http://www.hindawi.com/journals/ijdsn/2015/721921/
Environmental monitoring is a simple example of WSN application. You can make it 2D or 3D based on whether you include height of the sensor node from ground level along with the x,y coordinates or not?