Measuring connection quality?

I'm wondering what all of the factors to consider when measuring the quality of a connection.

There are a bunch of terms I've heard, all of which help determine whether or not there's a "good" connection: RTT/latency, jitter, packet loss. I'd like to read up on this - and I'm sure at every layer there are different factors - e.g. at layer 3/4 maybe you're dealing with ping, jitter and latency but at layer 1 you might be dealing with EM interference which obviously would affect the higher layers.

Can anyone point me in the right direction to read up on this a bit?

Also: are there any really good definitive software tools for breaking down the quality of a connection? I know iPerf is recommended by many as a good tool for measuring .. throughput? And obviously ping can measure RTT. What other tools are you guys using to quantify the quality of a connection?