IoT and full stack development is becoming more prevalent and DIY oriented. I would like to vet, discuss and collect active platforms projects, code, etc. outside of GitHub.
According to my simple knowledge, NS3 and NS2 are good platform for IP-WSN which is the most important element in IoT. Why this? Because you can find all the resources you need to implement your network regrading the IP-WSN .
Talking about data collecting, I got good results using Arduino to process data from sensors and using ESP8266-01 as a bridge to Wi-Fi networks. The version of SparkFun for ESP8266-01, known as "The Thing" was good to make a hub to other ESP8266-01 outside the range of wi-fi networks. But, we got some problems using AT commands to send requests to RESTful-based APIs.
Regarding to data analysis, instead using platforms as ThingSpeak, we created a dashboard, where data are shown in tables or graphics. We did it to customize to our data, but it was much more cheaper than ThingSpeak to our needs.
raspberry pi 3 by its supporting of range of tiny de sensors and communication modules, where it offer 1 Go of ram and 1GHz arm processor , wifi Bluetooth, and 40 pin to manage the add sensors, it is based in rasbian os (debian) with various programming lang support such as C C++ python java ,,etc, you can consider it as gateway, regular sensor , or sink,, etc
Regarding the data collection and analysis, things speak will be good. We have used Thingspeak platform and ESP8266 module for several projects.Thanks.
We have also used TETCOS NetSim extensively for our Under Graduate labs and for our R & D as well. Easy to use, powerful and has good support. I have heard OPNET is also good.