Skydock (Skydns) and Consul provide automagic service discovery primarily through dns. They use a strongly consistent backend (think Zookeeper or Etcd), to keep track of what servers are active and what applications they run. They then expose a DNS that routes through said servers. So lets say you had a client application that would talk to a node application that could be on any number of servers. What you could do is hard code that list into your application and randomly select one, in order to "fake" load balancing. However every time a machine went up or down you would have to update that list. What Consul provides is you just tell your app to connect to "mynodeapp.consul" and then consul will give you the proper address of one of your node apps.
Consul and Skydock are both applications that build on top of a tool like Zookeeper and Etcd. 
Finally all these tools, you can essentially consider "ops" tools to manage the lifetime of application, services and servers "in the cloud". What a developer ideally wants to do is just push code and not have to worry about what servers are running what, and worry about failover and the like. What Flynn provides (if I get it), is a diy Heroku like platform that makes use of tools like Etcd, Skydns, Docker(?) and others. With Flynn, I believe the goal is to radically simplify ops. Another project that I believe may be similar to Flynn is Apache Mesos.
 Technically Consul and Skydock, IIRC don't actually use Etcd or Zookeeper, but both implement an underlying protocol to achieve the same thing - Raft, but they could use Etcd or Zookeeper instead of implementing the protocol themselves.
But a good overview, thanks.