1. Micropolis -- https://code.google.com/p/micropolis/. This game is based on the source code of the original SimCity released under GNU GPL 3.0. Concincidentally, there's an ongoing effort to produce an HTML 5 port at https://code.google.com/p/microwebopolis/.
2. LinCity-NG -- http://sourceforge.net/projects/lincity-ng.berlios/. Looks and plays similar to SimCity 3000.
3. Simutrans -- http://www.simutrans.com/en/. This one is inspired by Transport Tycoon.
4. OpenTTD -- https://secure.openttd.org/www/en/. Same as above but requires Transport Tycoon Deluxe resources to run and might be closer to it in terms of mechanics.
[1] This is what I was half-hoping to see when I clicked the link. It would be really cool, and possibly profitable, for someone to quickly prototype one in HTML 5 in response to the SimCity 2013 fiasco.