The Many Observations of
Batman Begins
When he started working on this film, director Christopher Nolan along with David Goyer paid the offices of DC a visit to discuss what they could and could not do. In addition, Nolan did his research on Batman comics and books that have been released in the characters over 60 year history. The film does have several nods and references to the comics which are as follows. There are likely more that aren't on this list but contributions are greatly appreciated.
BATMAN: YEAR ONE - There are several references to Frank Miller's classic story
and are as follows
-Batman being pursued by a SWAT team at Arkham Asylum and then using the bats to
escape.
-The end scene with Gordon and Batman with a brief mention of the Joker
-Batman using a state of the art fabric to glide across Gotham
-The idea of Bruce using his own company's design and technology in his fight on crime was mentioned in Detective Comics 0, Batman: Secret Files and several other comics. The only difference is that even Lucius doesn't know about it.
-Alfred's speech about Wayne Manor being used to free slaves is based on Shadow of the Bat 45 where Bruce discovers his ancestor's efforts in freeing slaves
-Near the end of the film, we see how Gotham has gone from Mob rule to Freak rule just like it did in Long Halloween and Dark Victory
-Scarecrow is seen riding a horse in The Long Halloween. He also packs his drug in children's toys as he did in Dark Victory
-Gordon's first wife Barbara and son James Jr. can be seen briefly before Gordon's conversation with Batman outside his house
-Not exactly a comic reference but the scene where Officer Gordon tries to comfort Bruce almost happened in Sam Hamm's first draft of BATMAN. In that script Gordon was one of the first officers on the scene of the Wayne's death
-In the comics, a bat comes crashing through a window to give Bruce the inspiration for becoming Batman. A Bat does appear in the house but the scene in the cave with Bruce and the bats is very similar to how Tom Mankiewicz wrote the inspiration scene in his script.
-Arkham Asylum has been blown open twice. First in Batman 400 and the other was in Knightfall.
-The idea of Ra's using a decoy to conceal his true identity is in spirit of the character's first appearance where he faked Talia's kidnapping to test Batman.
-A lot of people have questioned the end scene where Batman leaves Ra's to die in the train. Batman did the same thing to the Joker in 'A Death in the Family' and left the KGBeast trapped underground in 'Ten Nights of the Best'
-Anyone notice the second Onesheet looks a lot like the cover of BATMAN 600 (Click to see larger versions)
Batman Begins Prequel???? Unfortunately, it seems that a lot of fans, non fans and film
critics have this misconception that Batman Begins is a prequel to the previous
four films. This is not correct as WB wanted a fresh new start with the Batman
series and that meant no ties whatsoever to the past films. By watching the film, a person should clearly get the
message that this film is not a prequel. Nonetheless, let's go over some scenes
which suggest why this film isn't tied to the others 
Batman Begins
BATMAN
The Waynes are shot and killed by Joe
Chill
The Waynes are shot and killed by Jack Napier
Batman befriends a young Sergeant James
Gordon in this film. Gordon is a street smart officer
"Commissioner Gordon" declares Batman to
be an outlaw until the end of the film. Gordon in this film comes off as a
bumbling twit
Gordon creates the Bat signal based on an
idea Batman used in the docks
Batman gives the Batsignal to the city and tells them to use
it when they need his help
Bruce is 29 when he becomes Batman
Bruce is 35 when he becomes Batman