There are two different episodes lists you may see. I will list them both in case of confusion. The first is the 100 episodes made in production and the second is a list of the order the episodes were originally aired (Note that the specials were originally aired as a TV Movies or Special length episodes and not split as there were after their first run on TV.
For a more detailed epiosde recap go to DuckTales Episodes @ TV.com
List of episode in production order (Specials split into single episodes), taken from DuckTales Web Site
(Episodes 1-5 are a 5 part mini-series)
1. "Don't Give up the Ship"
2. "Wronguay in Ronguay"
3. "Three Ducks of the Condor"
4. "Cold Ducks"
5. "Too Much of a Gold Thing"
6. "Armstrong"
7. "Luck o' the Ducks"
8. "'Til Nephews Do Us Part"
9. "Nothing to Fear"
10. "The Duck in the Iron Mask"
11. "Much Ado about Scrooge"
12. "Spies in their Eyes"
13. "Dime Enough for Luck"
14. "Jungle Duck"
15. "Scroogerello"
16. "Top Duck"
17. "Bermuda Triangle Tangle"
18. "The Status Seeker"
19. "Sweet Duck of Youth"
20. "Magica's Shadow War"
21. "Launchpad's First Crash"
22. "Home Sweet Homer"
23. "Duck to the Future"
24. "Down and out in Duckburg"
25. "Dr Jekyll and Mr McDuck"
26. "Time Teasers"
(Episodes 27-30 are a 4 part mini-series Catch as Cash Can, also known as the Fire Fruit Contest)
27. "A Drain in the Economy"
28. "A Whale of a Bad Time"
29. "Aqua Ducks"
30. "Working for Scales"
31. "Merit-time Adventure"
32. "Ducky Horror Picture Show"
33. "The Golden Fleecing"
34. "Horse Scents"
35. "Duckworth's Revolt"
36. "Ducks of the West"
37. "The Pearl of Wisdom"
38. "Once upon a Dime"
39. "Dinosaur Ducks"
40. "Sphinx for the Memories"
41. "Double-O-Duck"
42. "Microducks from Outer Space"
43. "Robot Robbers"
44. "Send in the Clones"
45. "The Lost Crown of Genghis Khan"
46. "The Right Duck"
47. "Back in the Outback"
48. "Sir Gyro de Gearloose"
49. "Raiders of the Lost Harp"
50. "Where No Duck Has Gone Before"
51. "All Ducks on Deck"
52. "The Curse of Castle McDuck"
53. "Superdoo!"
54. "Earthquack"
(Episode 55 is two stories in one regular half-hour episode)
55. "Magica's Magic Mirror/Take Me out of the Ballgame"
56. "Scrooge's Pet"
57. "The Money Vanishes"
58. "Back to the Klondike"
59. "Master of the Djinni"
60. "Launchpad's Civil War"
61. "Hero for Hire"
62. "Maid of the Myth"
63. "Hotel Strangeduck"
64. "Duckman of Aquatraz"
65. "The Uncrashable Hindentanic"
(Episodes 66-100 were produced for the 1989-1990 season)
(Episodes 66-70 are a 5 part mini-series Time is Money)
66. "Marking Time"
67. "The Duck Who Would Be King"
68. "Bubba Trubba"
69. "Ducks on the Lam"
70. "Ali Bubba's Cave"
71. "Attack of the 50-foot Webby"
72. "Ducky Mountain High"
73. "Yuppy Ducks"
74. "The Bride Wore Stripes"
75. "Bubbeo and Juliet"
76. "The Good Muddahs"
77. "Bubba's Big Brainstorm"
78. "Beaglemania"
79. "The Golden Goose, part one"
80. "The Golden Goose part two"
(Episodes 81-85 are a 5 part mini-series Super DuckTales)
81. "Liquid Assets"
82. "Frozen Assets"
83. "Full Metal Duck"
84. "The Billionaire Beagle Boys Club"
85. "Money to Burn"
86. "Metal Attraction"
87. "A Case of Mistaken Secret Identity"
88. "New Gizmo-kids on the Block"
89. "The Unbreakable Bin"
90. "Dough Ray Me"
91. "The Masked Mallard"
92. "Scrooge's Last Adventure"
93. "A Ducktales Valentine"
94. "Blue Collar Scrooge"
95. "Allowance Day"
96. "The Land of Tra-la-la"
97. "My Mother, the Psychic"
98. "The Big Flub"
99. "The Duck Who Knew Too Much"
100. "Attack of the Metal Mites"
Episodes Listed in their originally aired order (Taken from Bill Cotters, The Wonderful World of Disney Television)
Special Episodes or as normally referred to as TV Movies include Treasure of the Golden Suns, Time Is Money, Super DuckTales and The Golden Goose. The list is 87 episodes, counting each special as one episoe. These are listed in bold
1 Treasure of the Golden Suns
2 Send In The Clones
3 Sphinx For The Memories
4 Where No Duck Has Gone Before
5 Armstrong
6 Robot Robbers
7 Magica's Shadow War
8 Master Of Djinni
9 Hotel Strangeduck
10 The Lost Crown Of Genghis Khan
11 Duckman Of Aquatraz
12 The Money Vanishes
13 Sir Gyro de Gearloose
14 Dinosaur Ducks
15 Hero For Hire
16 Superdoo!
17 Maid Of The Myth
18 Down And Out In Duckburg
19 Much Ado About Scrooge
20 Top Duck
21 The Pearl Of Wisdom
22 The Curse Of Castle McDuck
23 Launchpad's Civil War
24 Sweet Duck of Youth
25 Earthquack
26 Home Sweet Homer
27 Bermuda Triangle Tangle
28 Microducks From Outer Space
29 Back To The Klondike
30 Horse Scents
31 Scrooge's Pet
32 A Drain In The Economy
33 A Whale Of A Bad Time
34 Aqua Ducks
35 Working For Scales
36 Merit-Time Adventure
37 The Golden Fleecing
38 Ducks Of The West
39 Time Teasers
40 Back In The Outback
41 Raiders Of The Lost Harp
42 The Right Duck
43 Scroogerello
44 Double-O-Duck
45 Luck o' the Ducks
46 Duckworth's Revolt
47 Magica's Magic Mirror/Take Me Out Of The Ballgame
48 Duck To The Future
49 Jungle Duck
50 Launchpad's First Crash
51 Dime Enough For Luck
52 The Duck In The Iron Mask
53 The Uncrashable Hindentanic
54 The Status Seeker
55 Nothing To Fear
56 Dr. Jekyll and Mr. McDuck
57 Once Upon A Dime
58 Spies In There Eyes
59 All Ducks On Deck
60 Ducky Horror Picture Show
61 'Till Nephews Do Us Part
62 Time Is Money
63 Super DuckTales
64 The Land Of Tra-La-La
65 Allowance Day
66 Bubbeo and Juliet
67 The Good Muddahs
68 My Mother, The Psychic
69 Metal Attraction
70 Dough Ray Me
71 Bubba's Big Brainstorm
72 The Big Flub
73 A Case Of Mistaken Secret Identity
74 Blue Collar Scrooge
75 Beaglemania
76 Yuppy Ducks
77 The Bride Wore Stripes
78 The Unbreakable Bin
79 Attack Of The 50-Foot Webby
80 The Masked Mallard
81 A DuckTales Valentine
82 Ducky Mountain High
83 Attack Of The Metalmites
84 The Duck Who Knew Too Much
85 New Gizmo Kids On The Block
86 Scrooge's Last Adventure
87 The Golden Goose
