Here is what the wiki has collected so far in terms of Morse Code:

Episode 1.01: The Pilot
Jericho Pilot

Episode 1.02: Fallout
Jericho Fallout

Episode 1.03: Four Horsemen
Jericho Three

Episode 1.04: Walls of Jericho
He knows Rob

Episode 1.05: Federal Response
There is a fire

Episode 1.06: "9.02"
The EMP hits

Episode 1.07: Long Live the Mayor
Pray for NYC

Episode 1.08: Rogue River
Rob not FBI

Episode 1.09: Crossroads
AOV Surprise
(Supposed to be NOV Surprise)
it is AOV, not NOV
AOV = Area of Vulnerability. In this episode, the AOV is the bridge, the surprise is Jonas and his men.

Episode 1.10: Red Flag


Episode 1.11: Vox Populi

(Vox Populi means "Voice of the People" in Latin)

Special Episode: Return To Jericho
back next week. 36 hours before bombs

Episode 1.12: The Day Before
Bloodshed

Episode 1.13: Black Jack
Bleeding KS
"Increased tensions over slavery led to the conflict and turmoil of 'Bleeding Kansas' and the Civil War." http://www.nps.gov/archive/fosc/bleeding.htm"During 'Bleeding Kansas', murder, mayhem, destruction, and psychological warfare became a code of conduct in Eastern Kansas and Western Missouri."

Episode 1.14: Heart of Winter
4 down 4 to go See the questions posted on Episode guide!

Episode 1.15: Semper Fidelis
They will need it

Episode 1.16: Winter's End
A costly deal

Episode 1.17: One Man's Terrorist
Rob Exposed

Episode 1.18: A.K.A.
Who Ran Red Bell

Episode 1.19: Casus-Belli
ONE GOT AWAY

Episode 1.20: One If By Land
We Pledge

Episode 1.21: Coalition of the Willing
Allegiance

Episode 1.22: Why We Fight
To the Flag