How could I ever have forgotten...
Timothy - The Buoys

Plus...
Bon Voyage - Kim Carnes
Sailin' - Kim Carnes
Cruisin' - Smokey Robinson
Cruising for Bruising - Basia
Anchorage - Michelle Shocked

"Shipyards Of New Zealand " by Midnight Oil (From the Red Sails in the Sunset album)
"Closer To Home/I'm Your Captain" by Grand Funk Railroad
"Six Months in a Leaky Boat" by Tim Finn, with The Wiggles
"The Ship Song" by Nick Cave (covered by Concrete Blonde with Steve Wynn)
"Big Canoe" by Tim Finn
"Shadow Captain" by CS&N
"Man Overboard" by Eric Clapton

Ship of Fools-World Party

And they also did "Yacht Dance"!

Another addition (and a personal favorite...)
Theme from Boat Weirdos - Joe Walsh

Ship in a Bottle - Beck
Ships (Where Were You) - Big Country
Broken Ship - Immaculate Machine
Girl Sailor - The Shins
Sail the Waterway - Steely Dan
Barnacle Bill the Sailor - Louis Prima and Keely Smith
Sail On - The Imperials
The Sailor's Song - The Stone Coyotes
Sailing By - Sinead Lohan

Sail on Sailor - Beach Boys

Sailing Homeward - Donovan

Row Jimmy--Grateful Dead
Navy Blue--Diane Renay
Stairway to Gilligan's Island--Little Roger & the Goosebumps ("Gilligan" theme sung to "Stairway to Heaven")
Nantucket Sleighride--Mountain
Shrimp Boats--Jo Stafford (one of my favorite songs as a little kid)
Crazy Water--Elton John (really about boats/whaling)
One of Our Submarines--Thomas Dolby
Dance Band on the Titanic--Harry Chapin
Sailor's Hornpipe--Mike Oldfield
Dock of the Bay--Otis Redding
Regatta De Blanc--Police
Yachting Types--The Yachts (bonus points)

Waiting for the Night Boat - Duran Duran

(Song and Artists) U-Boat - Woody Woodmansey's U-Boat

Beyond the sea - Ray Conniff Singers
Beyond the sea - Cliff Richard

album:

Regatta de Blanc - Police

artist:

Pablo Cruise
Julee Cruise

album cover:

I'll Sail My Ship Alone - Leon Russell

Downeaster Alexa - Billy Joel.

Sit Down, You're Rockin' the Boat--Don Henley et al. (from Guys and Dolls)
Man Overboard--Blondie
Night Boat to Cairo--Madness
Waiting on the Robert E. Lee--Al Jolson
On the Robert E. Lee--Neil Diamond (different song)
Don't Pay the Ferryman--Chris DeBurgh
Pirates--Emerson Lake & Palmer
Dixie Lily--Elton John (Dixie Lily: river boat)
Vahevala--Loggins & Messina

Sailing - Rod Stewart
Sailor - DERRINGER

Yellow Peril (Mina from China) - Steely Dan

Artist:

Byran Ferry

Land Ahoy - The Beach Boys

I would have contributed these if I had come by earlier.

Ship to Shore, Sailing Away, also by DeBurgh if no one mentioned those yet.

Panama Freighter, Ian Anderson (The Secret Language of Birds)
Burning the Boats, Madness
The Long Ships, Enya
There's a Boat That's Leavin' Soon for New York, Shirley Horn
Dreamboat Annie, Heart

Scatterbrain-Down With The Ship
Bad Brains-Sail On
Primus-Sailing The Seas Of Cheese
Deep Purple-Sail Away
Whitesnake-Sailing Ships
Big Country-Ships (Where Were You)
Blackfoot-Sail Away

Not my usual Milkmen post, but I can't resist....

"Junk" - Paul McCartney

"Take a Ride on a Riverboat" by Louisiana's LeRoux
"The Black Ship" by Shiva Burlesque
"Sinking Ships" by Sloan (from the album Navy Blues)
"Speedboat" by Lloyd Cole & The Commotions
"The Titanic" (also known as "It Was Sad When That Great Ship Went Down") -- old folk song

"Powderfinger" by Neil Young (Lyric "Look out, mama, there's a white boat comin up the river...")

ARTIST: Kayak
ARTIST: The Vulgar Boatmen