for me at least, just seeing numbers go up and get huge (Swarm Simulator) doesn't really do it for me. part of what makes Universal Paperclips so good is that, like Candy Box, a huge part of the joy is uncovering entirely new gameplay systems as you progress. A Dark Room was neat in that it brought the idea of a coherent narrative that you (sometimes subtly) uncover as you progress, too.
I feel like there's a lot of room left to explore in the space: different mechanics and systems to explore (outside of just clicking and upgrading), the possibility of cooperation with other players... the browser-based incremental game is pretty versatile in what it could do.
one of the most interesting one of these I've seen is Parameters (http://nekogames.jp/swf/prm.swf — download & play locally with Ruffle or some other SWF player). it's like an abstract RPG where you go on quests (or something) by clicking squares to fill them up. it's kinda crazy to me that nobody seems to have iterated on this concept.