Not necessarily best, but my favorites at this time.

1. Buckets of Rain
2. Simple Twist of Fate
3. Its All Over Now, Baby Blue
4. Percy's Song
5. All Along The Watchtower
6. She Belongs To Me
7. Like A Rolling Stone
8. Shelter From The Storm
9. Just Like A Woman
10. The Ballad Of Frankie Lee And Judas Priest
11. One More Cup Of Coffee
12. If You See Her, Say Hello
13. Idiot Wind
14. Mr. Tambourine Man
15. Blind Willie McTell
16. Ill Be Your Baby Tonight
17. Mama, You Been On My Mind
18. Sad Eyed Lady Of The Lowlands
19. Highway 61 Revisited
20. Lay Lady Lay

1. Like a Rolling Stone (the greatest rock song ever - in my opinion)
2. The Times They Are a-Changin
3. Desolation Row
4. Tangled Up in Blue
5. Lay Lady Lay
6. Subterranean Homeslick Blues
7. Just Like a Woman
8. Ballad of a Thin Man
9. The Lonesome Death of Hattie Carroll
10. Visions of Johanna

1. Hurricane
2. Like A Rolling Stone
3. Knockin' on Heavens Door
4. The Times They Are A-Changing
5. Blowin' in the Wind
6. Things Have Changed
7. Don't Think Twice, It's Alright
8. Desolate Row
9. Gotta Serve Somebody
10. It's Al2000l Over Now, Baby Blue
    There are some corners of the galaxy which have bred the most terrible things. Thing which act against everything we believe in. They must be fought-Second Doctor, The Moonbase.

Just off the top of my head, could be different tomorrow, and not in any order
Idiot Wind
Brownsville Girl
I Threw It All Away
Not Dark Yet
Huck's Tune
Tomorrow is a long time
Po' Boy
Precious Angel
Where are you tonight?
A Hard Rain's A-Gonna Fall

Spanish Harlem Incident
If You See Her (say hello)
Sooner or Later (One Of Us Must Know)
I Can't Believe you (She acts like we never met)
Isis
Silvio
Queen Jane Approximately
Jokerman
I'll Be Your Baby Tonight
Ballad of a Thin Man

Based on personal preference, without ranking them-
It's All Over Now, Baby Blue
The Times They Are A-Changin'
The Ballad of Hollis Brown
The Mighty Quinn
Percy's Song
Positively 4th Street
A Hard Rain's A-Gonna Fall
Song to Woody
Masters of War
Like a Rolling Stone
Always be yourself, everyone else is already taken.

10 that jumped into my head.
It's Alright, Ma (I'm Only Bleeding)
4th Time Around
Trying to Get to Heaven
Dark Eyes
Visions of Johanna
Chimes of Freedom
Tomorrow is a Long Time
Spanish Boots of Spanish Leather
One Too Many Mornings
Queen Jane Approximately

Like a rolling stone
how many roads
just like a woman
mr. tambourine man
the times they are a changin'
i want you
the hurricane
tangled up in blue
a hard rain gonna fall
desolation row

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1-Like a Rolling Stone
2-Blowing In The Wind
3-Mr. Tambourine Man
4-Just Like a Woman
5-Hurricane
6-Visions of Johanna
7-Shelter From The Storm
8-Desolation Row
9-The Times They Are A-changin'
10-Lay Lady Lay

Man, how do you decide.
10. The Times they are a-changing
9. The ballad of frankie lee and judas priest
8. Day of the locusts
7. Ballad of a thin man
6. Lily of the west
5. Isis
4. Desolation row
3. Man in the long black coat
2. Girl from north country

1. Billy 4
   Favourite album: Desire
   Beatles Song of the Day - http://twitter.com/BeatlesSotD

In no order:
Ballad of a Thin Man
Hurricane
Rainy Day Woman #12 & #35
Tangled Up in Blue
Like a Rolling Stone
Knockin' on Heaven's Door
Desolation Row
It's Alright, Ma (I'm Only Bleeding)
Mr. Tambourine Man
Visions of Johanna
"If you gotta go, go with a smile."- Jack Nicholson, Batman.

Girl from the North Country
A Hard Rain's A Gonna Fall
Masters of War
Maggie's Farm
It's Alright Ma (I'm Only Bleeding)
Highway 61 Revisited
Ballad of a Thin Man
Lay Lady Lay
Tangled Up in Blue
Simple Twist of Fate
Hurricane
Joey (yes I know Gallo wasn't Robin Hood but I like the song anyway)
You Ain't Goin' Nowhere
Ring Them Bells
Not Dark Yet

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Damn this is hard.

1. Masters of War
2. Let Me Die In My Footsteps
3. Blowin' In The Wind
4. The Times They Are A-Changin
5. Desolation Row
   6 A Hard Rains A-Gonna Fall
6. Song To Woody
7. Only A Pawn In Their Game
8. Just Like Tom Thumbs Blues
9. Like A Rolling Stone

1. Ballad of a Thin Man
2. The Lonesome Death of Hattie Carroll
3. Dirge
4. Knockin' On Heaven's Door
5. Blowin' In The Wind
6. Master of War
7. Forever Young
8. Day of the Locust
9. Love Sick
10. In My Time of Dyin'
    Janis Joplin, Jimi Hendrix, Joni Mitchell, and The Beatles all kissed Bob Dylan's ass.

How come no one has mentioned Ballad of Hollis Brown yet? Anyway the songs5b4 are in no particular order and are gems that tends to be overlooked in my opinion.
Bob Dylan's 115th Dream - Bringing It All Back Home
John Brown - MTV Unplugged
Abandoned Love - Biograph
Ballad of Hollis Brown - The Times They Are A-Changin'
I'm Not There - I'm Not There Soundtrack (the last song on Disc 2 IS Dylan)
Black Diamond Bay - Desire
Forgetful Heart - Together Through Life
Dirge - Planet Waves
Trying To Get To Heaven - Time Out Of Mind
Sign On The Window - New Morning

In no particular order:
Mr. Tambourine Man
Idiot Wind
Every Grain of Sand
The Lonesome Death of Hattie Carol
Tommorow is a Long Time
You're a Big Girl Now
Love Minus Zero/No Limit
Sad Eyed Lady of the Lowlands
Missisipi
My Back Pages
The signature below is false.
The signature above is true.

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The Times They Are a Changin'
Blowin' In The Wind
Chimes of Freedom
Mr. Tambourine Man
Subterranean Homesick Blues
Desolation Row
Girl From the North Country
Don't Think Twice It's Alright
Knockin' On Heaven's Door
A Hard Rain's A-Gonna Fall
People think I'm insane because I am frowning all the time

Desolation Row
My Back Pages
A Hard Rain's A-Gonna Fall
Stuck Inside of Mobile with the Memphis Blues Again
Where Are You Tonight? (Journey Through Dark Heat)
Brownsville Girl
Dark Eyes
Red River Shore
Changing of the Guards
Dignity
Honourable Mentions: Mississippi, Love Minus Zero/No Limit, Tangled Up in Blue, Shelter From The Storm, Farewell Angelina, Blind Willie McTell
"All the truth in the world adds up to one big lie"

• Bob Dylan

Favs at the moment
Chimes of Freedom
Grain of Sand
Forever Young
Workingman's Blues #2
Desolation Row
Buckets of Rain
Maggie's Farm
Love Minus Zero
Sad Eyed Lady.
Gates of Eden

Updated:

1. Desolation Row
2. Visions of Johanna
3. Like a Rolling Stone
4. Tangled Up in Blue
5. Blind Willie McTell
6. It's Alright, Ma (I'm Only Bleeding)
7. Mississippi
8. Subterranean Homesick Blues
9. Workingman's Blues # 2
10. With God On Our Side
    I'm A Lead Farmer, beep - Lincoln Osiris