How can I benchmark a router? I would like to measure total throughput between the router and the Internet, and between two computers on the network.
Well there's no easy way to "benchmark a router" if you want to test the bandwidth a computer behind the router, I'd check one of the bandwidth sites. Like speakeasy go there choose the closet city and run the test. Make sure you or anyone else on your LAN isn't streaming media or downloading something while the test is taking place. It takes a few minutes.
Typically there is no need to test the bandwidth between 2 computers on the same LAN unless you are experiencing problems. However it's pretty easy to do and is especially useful if you want to check throughput over a VPN. There's a program called QCheck that is free (you just have to fill out a form to download it). It's a quick install, just install the program on the 2 computers you are wondering about. Select the 2 endpoints you want to use, your localhost and the IP address of the other computer you installed QCheck on and choose TCP & Thoughput.
Here's there online help to that describes howto install, uninstall and use some of the other features.
Here's another way: Find a torrent with huge number of peers and try downloading it. Most distributions of GNU/Linux for example have such torrents. The advantage of using torrents it that they put heavier load at the router and some routers can choke on them, so if yours is one of them, you'll be able to find out. Also, torrents could take a while to download, so you can try out various QoS settings on your router and so on which usually can't be tested using Internet speed tests.
For testing transfer rate between two computers, I recommend Iperf. It ruins on most major operating systems and it uses data generated on the fly, so HDDs are not a limiting factor there. Here's an article showing where you can get windows version of Iperf.