Thor and Journey into Mystery are intertwined series. Thor (the character) started out in the anthology series Journey Into Mystery (1952) with issue #83, and took over the series with issue #125.
Marvel re-launched Journey Into Mystery a couple of times, and re-merged Thor and JIM a couple of times as well.
Marvel NOW starts off with a new Thor title (Thor: God of Thunder (2012)) and Journey Into Mystery (2012) #646.
Here is a table which updates the history of both Thor and JIM, as best as I can put together:
|Journey Into Mystery (1952)||1-125||125||1-125|
|The Mighty Thor (1966)||126-377||502||126-502|
|Journey Into Mystery (1972)||1-19||19||n/a|
|Journey Into Mystery (1996)||1-13||521||n/a|
|Journey Into Mystery (2009)||622-645||645||622-645|
|The Mighty Thor (2011)||1-22||22||n/a|
|Journey Into Mystery (2012)||646+|
Assuming this table is correct, Journey Into Mystery (1972); Journey Into Mystery (1996) and The Mighty Thor (2011) are all "orphaned" series with respect to issue numbering.