How to setup 6in4 tunnel? Say my Android device is on an IPv4-only network and I have a 6in4 tunnel (e.g. from HE/tunnelbroker.net) - how can I configure my device such that IPv6 traffic goes through that tunnel?

Background: on a stock Linux system you can connect to the 6in4 tunnel via issuing 5 iproute2 commands or so.
For that, I suggest you look at this application,isatapd (requires root).
It seems to match your description;


  ISATAP is a IPv6 in IPv4 tunnel mechanism that allows clients to get a
  global routeable IPv6 address over an IPv4 only network. The isatapd
  tool for Linux helps with the automatic configuration of the tunnel
  and the client endpoint and is shipped in this app and run as root.


Alternatively the same developer has a similar app IPv6Config (root required). From description;


  IPv6Config allows to configure some of the IPv6 kernel settings.
  Currently, it allows to automatically enable the "Privacy Extensions
  for Stateless Address Autoconfiguration in IPv6" as specified in IETF
  RFC4941 and implemented by the standard Linux kernel and to establish
  6to4 tunnels for IPv6 connectivity with providers that only provide
  IPv4 addresses so far.


Hope this helps