Many of these rare drops can be randomly (and rarely) found from any evil aligned NPC that is at least several tens of k in size, but rumor has it that not all of them can be collected this way.
The runes are often valued quite well, much better than most other random drops. Finding one can make a lower level player happy (given that s/he is able to kill ~50k+ evil NPCs in the first place). The prices can vary a lot though because of the nature of these items. During the years they've existed and as of October 2012, different runes have been heard being sold for anything between 50k to 36m. However it should be noted that the highest prices were mostly paid in the early days of Empyrean and the runes, when the stuff was new, rare and not everything was known about how it all works, so some resourceful highbies might've had gone into amusing little bidding frenzies in order to get their "last" rune...
List of Ancient runes: