1999: Prince (Bethel Farm 12/31/1999)
19th Nervous Breakdown: The Rolling Stones
54-46 Was My Number: Toots and the Maytals
ABC: Jackson 5
Afternoon at the Hillside: Bill Frisell
All of Me: Richard Rodgers and Lorenz Hart (? they wrote Blue Moon, etc, but not sure about All of Me or source here)
All of Me: Geral Marks / Seymour Simon (1931) / Irving Berlin Inc., also Billie Holiday / Lester Young. ABAC in BbM.
All Blues: Miles Davis
Amazing Grace: John Newton (hymn 1772; appears on 10/10/1998 Williams College)
Antes de Haber Mundo: Ramito
Any Major Dude Will Tell You: Steely Dan
Anything You Want: Daniel Britt / Spoon (4/28/2007)
Baba O'Reilly: The Who
Black Cow: Steely Dan
The Boy in the Bubble: Paul Simon (7/3/2008, 8/13/2021)
Bright-Size Life: Pat Metheney
Brooklyn (Owes the Charmer Under Me): Steely Dan 
Brown-Eyed Women: Grateful Dead (U Wisc. 10/9/1999)
Burning Down The House: The Talking Heads
By the Rivers of Babylon: Dowe / McNaughton / Farian / Reyam (The Melodians, 1970) 
Camarillo Brillo: Frank Zappa
The Cape Verdean Blues: Horace Silver
Carry the Zero: Built to Spill
Celebration: Kool and the Gang
Changes: David Bowie (12/31/2006)
Cissy Strut: The Meters
Come Back Baby: Ray Charles (High Sierra 7/5/2015)
Come Together: The Beatles (12/30/2006)
Cool #9: Joe Satriani 
Crosstown Traffic: Jimi Hendrix
Cupid: Sam Cooke (12/8/2006)
Dark Blue: John Scofield
Dark Star: The Grateful Dead
Don't Think Twice, It's Alright: Bob Dylan
Do It Again: Steely Dan
Down Under: Men at Work
Drown in My Own Tears: Ray Charles
Ego Tripping at the Gates of Hell: The Flaming Lips
Else: Built To Spill
Enter Sandman: Metallica (7/30/1999 Living Room)
Everybody Wants to Rule the World: Tears for Fears
Fancy Glass: Leslie Helpert
Feelin' Alright: Dave Mason (Traffic, 1968)
Fight Test: The Flaming Lips
The Gambler: Don Schlitz (Kenny Rogers, 1978) 
Girls Just Wanna Have Fun: Cindy Lauper
Green Earrings: Walter Carl Becker / Donald Jay Fagan (Steely Dan, 1976)
Hallelujah: Leonard Cohen
Happiness is a Warm Gun: The Beatles
Have You Ever Seen the Rain?: Creedence Clearwater Revival (1971)
Heart and Soul: Mike Chapman / Nicky Chinn (Exile, 1981 / Huey Lewis, 1983)
Heart-Shaped Box: Nirvana
Heartbreaker: Led Zeppelin
Hello Sunshine: Aretha Franklin
Hells Bells: AC/DC
Hold On: Tom Waits (12/30/2011: Cafe Du Nord)
Human Nature: Michael Jackson (1/27/2000)
I Heard It through the Grapevine: Marvin Gaye
I Want You Back: Alphonso J Mizell / Berry Jr Gordy / Dennis Lussier / Freddie Perren (Jackson 5, 1969)
I want A New Drug: Huey Lewis
Imagine: John Lennon
Impressions: John Coltrane
In The Light: Led Zeppelin
In Russia With Love: The Skatellites
It's a Long Way to the Top (If You Wanna Rock 'n' Roll): AC/DC (12/8/2006, 12/31/2006)
It's Alright Ma, I'm Only Bleeding: Bob Dylan
It's Only Rock and Roll (but I Like It): Jagger / Richards (The Rolling Stones, 1974) 
Island of Peace: Melodians (1/31/1998 Common Ground)
Jealous Guy: John Lennon (2000)
Juicy Fruit jingle (unknown author, 1986)
Jumpin' Jack Flash: The Rolling Stones
Just a Closer Walk With Thee: traditional
Kid Charlemagne: Steely Dan
King of Pain: The Police
Land Down Under: C. Hay / R. Strykert (Men Without Hats, 1981)
Late in the Evening: Paul Simon
Let The Music Take Your Mind: Kool and the Gang
Little Lulu: Jules Leonard "Buddy" Kaye / Fred Wise / Sidney Lippman (Bill Evans 1964) 
Livin' Lovin' Maid: Led Zeppelin
Living on a Prayer: Bon Jovi (1986)
Louis Collins: Mississippi John Hurt (Ashland 9/24/2000)
Lullaby of Birdland: George Shearing (1952)
Macarena: Los Del Rio
Makin' Whoopee: Gus Kahn / Walter Donaldson (Eddie Cantor orig. 1928, appears on 2/20/1998 Weaton College)
Man in the Mirror: Michael Jackson
Marie's the Name: Elvis Presley
Maybelline: Chuck Berry
Moby Dick: Led Zeppelin (1969)
Modern Love: David Bowie (1983)
Money Money Money: Nathan Moore
Mood Indigo: Duke Ellington
Moonlight Mile: Jagger / Richards (Rolling Stones, 1971)
Mother Popcorn: Alfred James "Peewee" Ellis / James Brown (1969)
Nica's Dream: Horace Silver
Night Shift: Bob Marley
Night in Tunisia: Dizzy Gillespie (2/20/1998 Wheaton College)
No Quarter: Led Zeppelin
Nostalgia in Times Square: Charles Mingus
Ode to Joy (9th Sympony): Ludwig von Beethoven
One Love: Bob Marley / Curtis Mayfield
Only Love Can Break Your Heart: Neil Young (3/22/2006)
Owner of a Lonely Heart: Yes
PYT: Michael Jackson
Paint It Black: The Rolling Stones
Pass It On: Bob Marley / Bunny Wailer
Pretty Young Thing: Michael Jackson
Pretzel Logic: Steely Dan
Proud Mary: Creedence Clearwater Revival
Pungee: The Meters
Ramona: Bob Dylan
Rastaman Chant: Bob Marley
Rhythm-a-ning: Thelonious Monk
Ride On: AC/DC
Rock and Roll: Led Zeppelin
Rustic Hop: Bob Brookmeyer / Stan Getz
Scarlet Begonias: The Grateful Dead
St. Thomas: Sonny Rollins (1956)
Shake Everything You Got: Maceo Parker
She Caught the Katy: James A Rachell / Taj Mahal  
The Sidewinder: Lee Morgan (1963, appears on 2/20/1998 Wheaton jazz night)
Sleep Walk: Santo and Johnny (Berkfest 2003)
Smells Like Teen Spirit: Nirvana (BB King's 12/31/2008)
So What: Miles Davis
Something's Got to be Arranged: Paul Geremia
Southbound: Allman Brothers
Stand By Me: Ben E. King / Jerry Leiber / Mike Stoller
Stayin' Alive: Bee Gees
Steppin' Out: Joe Jackson
Straight, No Chaser: Thelonious Monk
Summertime: George and Ira Gershwin (from Porgy & Bess)
Superstition: Stevie Wonder
Sway: Rolling Stones (3/30/2006)
Sweet Georgia Brown: Ben Bernie / Maceo Pinkard / and Kenneth Casey 
Sweet Thing: Van Morrison
Take The Coltrane: Duke Ellington
Tempted by the Fruit of Another: Difford / Tillbrook (Squeeze, 1981)
Tenor Madness: Sonny Rollins
The Chicken: Pee Wee Ellis
The Lemon Song: Led Zeppelin
The Sidewinder: Lee Morgan
The Song is You: Jerome Kern
The Thumb: Wes Montgomery
The Times They Are A-Changin': Bob Dylan
Third Stone from the Sun: Jimi Hendrix (1/28/2000)
This Land is Your Land: Woodrow Wilson "Woody" Guthrie (1940)
Thriller: Michael Jackson
Tin Can Coffee Cup: Nathan Moore
Tomorrow Never Knows: The Beatles (Lennon/McCartney)
Tumblin' Dice: The Rolling Stones
Uptight (Everything's Alright): Stevie Wonder
Wade in the Water: traditional
War: Bob Marley (Rastaman Vibration 1976; appears on 3/7/1998 CMU)
Watermelon Man: Herbie Hancock
Won't Get Fooled Again: The Who
The Weight: Jaime Royal "Robbie" Robertson (The Band, 1968) 
What Is and What Should Never Be: Led Zeppelin 
What's So Funny about Peace, Love and Understanding?: Elvis Costello
Where's My Mind: Pixies (6/23/2007, 6/25/2007)
While My Guitar Gently Weeps: George Harrison
Wish You Were Here: Pink Floyd (High Sierra 2022)
With or Without You: U2
Wonderful World: Sam Cooke (3/22/2006, 3/30/2006)
The Yipiyuk: Shel Silverstein
You and the Night and the Music: Howard Dietz / Arthur Schwartz / arr. by Jack Cortner 
You Can Call Me Al: Paul Simon