I've started listing the songs for each episode in the Episode section of the forums to make it easier for people to find what they're looking for.  If you're searching for a song from a particular episode (season 2), check the forum for each episode here.

I will post a "master list" of sorts here:

Episode 201: "Deep in Death" (Season Premiere)

Junior Senior, "Can I Get Get Get" – Buy Now
Opening shot & Castle photo shoot

The Datsuns, "Highschool Hoodlums" – Buy Now
NYPD busts some small time drug dealers  

DJ Dimi, "River To Your Soul" – Buy Now
Castle enters an underground poker game in the bowels of Chinatown  

Charles Fearing, "50-96″ –  
Castle get deeper into underground poker game  

Lex Land, "My Fault, Your Mistake" – Buy Now
Castle goes to precinct and apolgizes to Beckett.

Episode 202: "The Double Down" – Music

Sloan, "Who Taught You To Live Like That?" -Buy Now
Opening scene, boisterous activity at the precinct.

Actionslacks, "We Are Not The Losers (Anymore)" – Buy Now
NYPD busts some small time drug dealers

Episode 203: "Inventing The Girl" Music

Jaconfetti, "We Swing"
A couple skinny dips in a fountain and discovers a dead body

Madison Park, "My Personal Moon" – Buy Now
Backstage at Teddy Farrow Fashion Show

Ultraviolet Sound, "In A Magazine"
Rooftop Photo Shoot

Mahjong & D'Layna, "So Thankful (Original Instrumental Mix)" – Buy Now
Club Photo Shoot

Chad Hannah, "Friends Forever More"
Martha longs for the past

Lindsey Katt, "Heart Place"
Loft, Rina arrives, show closer

Episode 204: "Fool Me Once" Music

Winter Gloves, "Factories" – Buy Now
International School classroom, first graders settle in to watch a video

Mozella, "Can't Stop" – Buy Now
Beckett in bubble bath w/ wine & Castle novel.

PD, "Twinkle Twinkle Little Star"
Castle comes home, hears violin lesson, it's Martha getting the lesson instead of Alexis.

Episode 205: "When The Bough Breaks"

Alyx, "Fever's Burning Up" – Buy Now
Opening scene where Castle's book agent wakes him up at 7am

OneRepublic, "Everybody Loves Me" – Buy Now
Beginning of the book launch party

El Presidente, "Rocket" – Buy Now
Beckett reads the dedication at the book launch party

Episode 206: "Vampire Weekend"

Moloko, "Pure Pleasure Seeker" – Buy Now
Castle's Loft Party

Episode 207: "Famous Last Words"

Anna Waronker, "Threshold"

Anna Waronker, "Underground"

Anna Waronker, "Here Kitty Kitty"

Episode 208: "Kill The Messenger"

Locksley, "I'm On Fire"
Opening Scene when the messenger is riding his bike

Salme Dahlstrom, "Coming Fast, Coming Hard"
Mamma's on the prowl – Martha leaving for her date

Episode 209: "Love Me Dead"

The Thermals, "Now We Can See" – Buy Now

The Emeralds, "Love Fire" – Buy Now

The Gun Shys, "Madly In Action" – Buy Now

Swingfly, "Winner" – Buy Now

Vetiver, "Everyday" – Buy Now

Episode 210: "One Man's Treasure"

Brakesbrakesbrakes, “Crush On You” – Buy Now

Regina Spektor, “The Calculation” – Buy Now

Mad Langer, “I’m Still Fact, She’s Fiction”

Episode 211: "The Fifth Bullet"

Jenni Alpert, "All We Need Is Love" Buy Now
"Who knows, I like him and he likes me and that's enough" family back together moment.

Amy Stroup, "Chin Up" Buy Now
Final scene with Castle & Martha