For the sake of simplicity I'm only including individual songs once (i.e. Visions of Johanna is listed, so you won't find the acoustic version of the song, Freeze Out, elsewhere on the list). The same goes for basically-the-same-songs, like New Danville Girl and Brownsville Girl.
100. Ring Them Bells
99. Jokerman
98. Only a Pawn in Their Game
97. Too Much Of Nothin'
96. Talkin' John Birch Paranoid Blues
95. To Be Alone With You
94. Precious Angel
93. Workingman's Blues #2
92. Meet Me In the Morning
91. On A Night Like This
90. Absolutely Sweet Marie
89. Tiny Montgomery
88. You're Gonna Make Me Lonesome When You Go
87. Senor (Tales of Yankee Power)
86. Million Dollar Bash
85. The Times They Are A Changin'
84. Hurricane
83. On the Road Again
82. Tweedle Dee & Tweedle Dum
81. I and I
80. Bob Dylan's 115th Dream
79. Talkin' Bear Mountain Picnic Massacre
78. It Takes A Lot to Laugh, It Takes a Train to Cry
77. New Morning
76. Tonight I'll Be Staying Here With You
75. Forever Young
74. Mississippi
73. Quinn the Eskimo (The Mighty Quinn)
72. John Wesley Harding
71. Highlands
70. Thief on the Cross
69. Mr. Tambourine Man
68. I Shall Be Released
67. You Ain't Going Nowhere
66. Sign on the Cross
65. Can You Please Crawl Out Your Window
64. Not Dark Yet
63. Thunder on the Mountain
62. All Along the Watchtower
61. Caribbean Wind
60. Ballad of a Thin Man
59. Day of the Locusts
58. Don't Think Twice, It's All Right
57. Isis
56. A Hard Rain's A-Gonna Fall
55. Po' Boy
54. New Pony
53. To Ramona
52. It's All Over Now, Baby Blue
51. Subterranean Homesick Blues
50. Desolation Row
49. Goin' to Acapulco
48. Maggie's Farm
47. I'm Not There
46. Simple Twist of Fate
45. If Not For You
44. Everything Is Broken
43. Blind Willie McTell
42. It's Alright Ma (I'm Only Bleeding)
41. Stuck Inside of Mobile With The Memphis Blues Again
40. Blowin' In The Wind
39. Gates Of Eden
38. Series Of Dreams
37. Masters Of War
36. She's Your Lover Now
35. With God On Our Side
34. Romance In Durango
33. It Ain't Me Babe
32. Buckets of Rain
31. The Groom's Still Waiting at the Altar
30. Most Of The Time
29. One More Cup Of Coffee
28. Make You Feel My Love
27. Shelter From The Storm
26. Most Likely You Go Your Way (And I'll Go Mine)
25. She Belongs To Me
24. Ballad of Frankie Lee and Judas Priest
23. Queen Jane Approximately
22. Love Minus Zero/No Limit
21. Sign On The Window
20. Every Grain Of Sand
19. Girl From The North Country
18. New Danville Girl
17. Last Thoughts On Woody Guthrie
16. All I Really Want To Do
15. Positively Fourth Street
14. As I Went Out One Morning
13. Sad Eyed Lady of the Lowlands
12. Talking World War III Blues
11. One Of Us Most Know (Sooner Or Later)
10. Lily, Rosemary And The Jack Of Hearts
9. I Want You
8. Visions of Johanna
7. The Lonesome Death Of Hattie Carroll
6. Lay Lady Lay
5. Idiot Wind
4. Knockin' On Heaven's Door
3. 4th Time Around
2. Tangled Up In Blue
1. Like A Rolling Stone
