What's the real difference between throughput and capacity of a network cable? I was preparing a presentation in work on GPON &amp; other optical network technologies using documentation provided by a supplier, and the claim it made was "GPON networks have a capacity of up to 100Tbps".

Instantly that looked odd to me as I know the throughput of the most advanced version of InfiniBand only goes up to 280-290Gbps. I couldn't find any evidence that supported the supplier's claim, only turning up that the throughput of GPON was up to 2.5Gbps. The colleague who had been given the documentation I was working off said that the supplier had claimed that speed was independent of the devices on the network, and that it was limited only by the Optical Network Units (ONUs) and endpoint devices.

That seems a bit ridiculous considering the "data" in an optical cable is a pulse of light. Light travels (in a vacuum) at c, so surely the speed of any fibre-optic network is close to c, and in the same way the speed of electromagnetic wave propagation down a wire is 66 - 99% the speed of light, but I've never heard a CAT5 manufacturer claim their cables can support those speeds.

I brought it up with the supplier rep and he (derisively) let me know that "that's the capacity, not the throughput". I'm aware that to a lot of people the terms are interchangeable, but from a technical standpoint if throughput is the amount of data that can be sent over a network in a specified amount of time, what is capacity?

It would seem like the "capacity" of an optical fibre is "1 flash of light" as that's all it's likely to hold.

NB this question is about the science behind computer (or other data) networks, so I think it belongs here, despite references to particular hardware.
"Capacity", similar to many other terms, is a an overloaded word. In the example you bring, it seems that the meaning is equivalent to "throughput", i.e., the maximal "amount" of information a channel/network/etc. can transfer per time unit. 

However, while these terms can be used interchangeably, to my ears "capacity" has the feel of a theoretical limit, while "throughput" has a feel of a practical limit. As in: "the capacity of a fiber channel is 1Gb/sec, which (due to coding, errors, and technical limitation)  leads to a maximal throughput of 986KB/sec (=of YOUR data)". 

A different explanation which may be used in other settings is a one in which the capacity of a link is measured in relative terms, that is, it will be a ratio between 0 and 1, to be multiplied with a predefined  maximal rate of information transfer. This notation is useful when computing flows over the network.