Trousers were originally two separate garments so, unless you'd lost a leg in battle or whatever, they would typically come as a pair. This expression remained even when they began to be a single garment. By extension, any garment which was worn by pulling it over the feet also became 'a pair of', hence a pair of knickers.
Similarly, glasses were two pieces of glass so, unless you wore a monocle, they also came in pairs, even after they were joined across the bridge of the nose.
Scissors are made up of two blades, so the phrase 'a pair of scissors' is not so easy to etymologise.
http://en.wiktionary.org/wiki/scissor
What about a pair of compasses...?