I have to qualify this by saying I've been running over 40 years, so I've seen a lot of change in shoes/clothes; runners nowadays probably can't imagine the stuff we used to have to use (just as I can't imagine the things runners in 40s/50s used).
That being said, my three favorite innovations:
1. Nylon shoe uppers: when I started, shoes were pretty much either leather or canvas, and the latter only very low end. The leather uppers took a while to break-in, assuring lots of blisters. And when they got wet, they stayed wet! When Tiger came out with their first nylon uppers, I was hooked immediately - lighter, quicker to dry, no blisters.
2. Polypropylene: Again, sweatsuits were usually cotton -- not very warm, and they got sopping wet. The first wave of polypropylene tights & uppers immediately made winter running much better -- I could wear much less, be warmer, and when it got wet it didn't stay wet. I've stayed loyal to it, but it's harder & harder to find.
3. Running hats: I wear glasses, so running in rain or snow was at best annoying and at worst dangerous, as the precip would get all over my glasses & fog them up too, making visibility a bother. Amazingly, I only started wearing a hat in precip in the last few years, and it is SO much better...I don't know why I waited so long.
I suppose gore-tex deserves an honorable mention, but I rarely wear it -- I'm not one for rainsuits.
Other favorites?