The flag issue was one. Rutherford presented (and lost) the Gobitas case as freedom of religion. In Barnette, Franz/Knorr/Covington reinvented it as a 1st Amendment case of freedom of speech, which they won.
edit to add: Identifying as a 'religion'. Under Rutherford, all 'religion' was a snare and a racket. We are not a religion, have no clergy or creed. About 1950, (a dark blue book, I forget the name of it) Franz et al changed it to 'there is true religion and false religion'. I believe this one falls under the umbrella of doctrinal changes to support draft exemption claims. All JW men are 'ministers', so they had to identify as a religion in the government's eyes.