World's Finest Comics #3 (Fall 1941) - The Scarecrow's First Ever Appearance! You'll most likely find this in reprint in one of the Batman Chronicles volumes.
Detective Comics #73 (Mar. 1943) - The second appearance and the last for over 20 years
Batman #189 (Feb. 1967) - This comic features the first appearance of the Master of Fear in over 20 years and is also his first Silver Age appearance. Isn't to pricey yet so I would really urge you to try and a find the actual comic. Nothing like actually holding the real thing.
Batman #200 (Mar. 1968) - The Scarecrow gets to star as the villain in the big anniversary issue of Batman.
The Brave and the Bold #197 (April 1983) - The Golden Age Batman and Catwoman of Earth 2 go up against the Master of Fear himself!
Batman #457 (Dec. 1989) - Batman and Vikki Vale are captured by The Scarecrow and it is up to one person to help them, Tim Drake. This comic involves lots of the Scarecrow and makes him the first Bat rogue Tim goes up against. A must have issue if you are not only a Scarecrow fan, but a Tim Drake fan as well.
Knightfall (1993) - A huge story arc that broke out everyone at Arkham and gave us the character Bane! This story arc a good amount of Scarecrow in it and he is often paired up with the fellow mad man, The Joker. Can fine in reprint collection book or possibly in the back issue box of your comic book store.
Batman Annual #19 (1995)- This gave us the most known origin of the Master of Fear.