Lets try this as a means to detect non-neutral throttling:
1) During a none peak time period download a video from a popular site that may be competing against your ISP's video service.
2) Set up a VPN and repeat via the VPN.
3) If the VPN download is significantly quicker then it is likely your ISP throttling certain sites.
4) Compare notes with other users of your ISP to establish a pattern.
I suppose someone could write a program to automate the above with a few extras and for various services.