The first one being AllSeen Alliance [1] supported by Qualcomm, and the second one being Open Interconnect Consortium [2] lead by Intel.

The difference seems that The Thread Group is solely focusing on the network protocol [3] and not a full IoT platform like AllSeen and OIC.

And apparently, Nest thermostats are already running a version (is it the final one?) of the Thread protocol.

[1] https://allseenalliance.org/

[2] http://www.openinterconnect.org/

[3] http://www.threadgroup.org/Technology.aspx