Riddle of the Human Scarecrow
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.
Batman with Robin - The Boy Wonder: The Scarecrow Returns
Detective Comics #73 (Mar. 1943) - The second appearance and the last for over 20 years
Fright of the Scarecrow
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.
The Man Who Radiated Fear
Batman #200 (Mar. 1968) - The Scarecrow gets to star as the villain in the big anniversary issue of Batman.
Batman and Catwoman: Night of Passion, Night of Fear
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!
Master of Fear
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.
Scarecrow: Master of Fear
Batman Annual #19 (1995) - This gave us the most known origin of the Master of Fear.
The Long Halloween: Punishment
Batman: The Long Halloween (1996-1997) - The origin tale of Two-Face also includes some very fine appearances of the Scarecrow as well as others of the Bat rogues.
No Man's Land
Batman: No Man's Land #1 - Volume 1 - This has him taking refuge in a church and manipulating the inhabitants after an earthquake hits Gotham.
Dark Victory: Toys
Batman: Dark Victory (1999-2000) - The follow up to Long Halloween has excellent Scarecrow appearances and #3 of this mini series even has a killer Scarecrow cover and has Scarecrow as the main focus villain of that one book. A read for Bat fans of every type not just Scarecrow! It includes great Batman, Two-Face, Joker, Grundy, the Gotham Crime Families, Riddler, Catwoman, Poison Ivy, Alfred, and even gives us a modern retelling of the origin of Dick Grayson!
Hush: The Grave
Batman: Hush (2002) - Scarecrow is revealed to have interned at Arkham. While interning he met Thomas Elliot (Hush) and taught him the power of fear which will be part of the Hush's crime. He even uses the Scarecrow to go up against the Caped Crusader.
As the Crow Flies
Batman #626 to #630 (2004) - The Scarecrow becomes the Scare Beast. I don't really care for it, but it has been one of the most recent Scarecrow storylines.
Face the Face
Detective Comics #820 (August 2006) - Scarecrow brings Batman and Robin (Tim Drake) face to face with some of their deepest fears.
Blackest Knight (2009) - In this Green Lantern storyline that involved much of the DC universe the Scarecrow joins the Sinestro Corps due to his need of fear.
Cycle of Violence
Batman, The Dark Knight #10-15 (2012) - The Scarecrow has returned to Gotham City, but he's no longer the meek punching bag Batman is used to. The villainous genius has always preyed on the worst fears of his victims, but has refined his legendary fear toxin to even greater effectiveness and deadlier consequences. As the Scarecrow's origin is unfurled, Batman must find out not only how to conquer this dangerous psychopath, but how to beat his own worst fear.