I think molten and plague both stack, and molten can actually stack with itself (for example if a champ runs over it's previous path and you're standing on the intersection. This can be a real problem when you have a champ running in circles around you.
The one that does more damage the longer you stand in it is desecration.
WHOOPS. I was thinking of desecrator instead of molten. Molten definitely stacks. If you've ever fought against horde/molten it is really apparent that the trails are doing more than normal DoT.
Those huge spinning blade guys can stack them without moving too which is a real PITA.