Hi, and welcome to Seibertron.com!
If you're starting afresh, and don't want to run too far back, I'd say go with Robots in Disguise and More than Meets the Eye alongside each other - both leading into Dark Cybertron, and then branching out again next month. If you want to go further back, try Autocracy and then Monstrosity, which have some 'origin' stories of sorts, and both of which more or less tie in with the main continuities.
BUT if you're feeling brave...
The overall IDW-verse is as follows.
I. The Beginning…1. Megatron Origin
2. Spotlight - Orion Pax
3. Spotlight – Blur (All Hail Megatron Vol. 3 p. 4)
4. Autocracy
5. Monstrosity
6. Primacy in 2014
7. Spotlight - Thundercracker
II. The Spotlights8. Spotlight – Shockwave (Spotlight Vol. 1 p. 9)
9. Spotlight – Cliffjumper (All Hail Megatron Vol. 3 p. 52)
10. Spotlight – Soundwave (Spotlight Vol. 2 p. 9)
11. Spotlight – Wheelie (Spotlight Vol. 3 p. 100)
12. Spotlight - Hot Rod (Spotlight Vol. 1. p. 50)
13. Spotlight – Sixshot (Spotlight Vol. 1 p. 73)
14. Spotlight -- Ultra Magnus (Spotlight Vol. 1 p. 96)
III. Present Day Earth15. Infiltration #0-3 (through p. 86)
16. Stormbringer #1-3
17. Infiltration #4-5 (p. 87-132)
18. Stormbringer #4 (Full page panel of Thunderwing in jet mode)
19. Infiltration #6 (p. 133 to end)
20. Spotlight – Kup (Spotlight Vol. 2 p. 28)
21. Escalation #1-2 (through p. 46)
22. Spotlight – Nightbeat (Spotlight Vol. 1 p. 27)
23. Escalation #3-6 (p. 47 to end)
24. Spotlight – Ramjet (Spotlight Vol. 2 p. 100)
25. Spotlight - Optimus Prime (Spotlight Vol. 2 p. 76)
26. Spotlight – Galvatron (Spotlight Vol. 2 p. 52)
27. Devastation #1-4 (pages unnumbered; Chapter 4 ends with close-up of Starscream talking to Astrotrain)
28. Spotlight – Blaster (Spotlight Vol. 3 p. 4)
29. Spotlight – Arcee (Spotlight Vol. 3 p. 28)
30. Devastation #5-6 (pages unnumbered; Chapter 5 begins with “Cybertron-The Past”)
31. Spotlight – Mirage (Spotlight Vol. 3 p. 76)
32. Spotlight – Grimlock (Spotlight Vol. 3 p. 52)
33. Spotlight Volume 4 – Revelation
34. Maximum Dinobots
IV. All Hail Megatron!35. All Hail Megatron Vol. 2 Chapter 2 p. 1
36. All Hail Megatron Vol. 2 Chapter 1 p. 3-13, 17-19
37. All Hail Megatron Volume 4: “Everything In Its Right Place”
38. Spotlight – Drift (All Hail Megatron Vol. 3 p. 76)
39. Spotlight – Metroplex (All Hail Megatron Vol. 3 p. 100)
40. All Hail Megatron Volume 4: “Lost And Found”
41. Spotlight- Jazz (All Hail Megatron Vol. 3 p. 28)
42. All Hail Megatron Volume 1-2 in full
(Note: All Hail Megatron Volume 4 has #43-#48)
43. “Old Ways” Optimus/Ironhide
44. “Uneasy Lies The Head” Starscream
45. “Replay” Sunstreaker
46. “Rebirth” Galvatron/Cyclonus/Scourge
47. “The Man Of Steel” Spike
48. “Hidden” Bumblebee
V. Three Years Later (Note: #50-#58, #68-#72 are located in Last Stand Of The Wreckers Hardcover)
49. Spotlight- Prowl (Ongoing Vol. 6)
50. Autobot File: Rotorstorm p. 130
51. Autobot File: Pyro p. 131
52. Autobot File: Guzzle p. 132
53. Autobot File: Ironfist p. 133
54. Autobot File: Impactor p. 134
55. Decepticon File: Snare p. 135
56. Decepticon File: Overlord p. 136
57. Squadron X p. 161
58. BULLETS/OUT OF BULLETS: Deleted Scenes p. 116 - 128 except ‘Nine Months Later’
59. Last Stand Of The Wreckers #1
60. Ongoing Vol. 1 For All Mankind #1
61. Last Stand Of The Wreckers 2-3
62. Ongoing Vol. 1 #2
63. Last Stand Of The Wreckers 4
64. Ongoing Vol. 1 #3-4
65. Bumblebee paperback
66. Ongoing Vol. 1 #5-6
67. Last Stand Of The Wreckers 5
68. ESCAPE p. 162
69. ZERO POINT p. 170
70. IN WORD AND DEED p. 175
71. BULLETS: Nine Months Later p. 125
72. Wreckers Mosaic Dead Man’s Boots p. 129
73. Ironhide paperback
74. Drift paperback
75. Ongoing Vol. 2 International Incident (#7-#8)
76. Ongoing Vol. 4 Heart Of Darkness.“The Road To CHAOS”. Infestation occurs towards end of #4. End of #4 lines up with end of Ongoing #20 in Ongoing Vol. 5: Chaos Theory.
77. Infestation Transformers 1-2
80. Ongoing Vol. 2 #9 to #12
81. Ongoing Vol. 3 Revenge of the Decepticons #13
82. Spotlight - Megatron
83. Ongoing Vol. 3 remainder of Revenge Of The Decepticons
84. Ongoing Vol. 5 Chaos Theory through end of Police Action: Prolog
85. Spotlight - Bumblebee
86. Ongoing Vol. 6 Police Action
87. Ongoing Vol. 5 remainder of Chaos Theory
88. Ongoing Vol. 7 CHAOS
89. Death Of Optimus Prime (More Than Meets The Eye Vol. 1)
VI. The Autobots Divide90. More Than Meets The Eye Ongoing #1 with Rodimus (Vol. 1)
91. Robots In Disguise Ongoing #1 with Bumblebee (Vol. 1)
92. MTMTE #2-3 (Vol. 1)
93. RID #2-3 (Vol. 1)
94. MTMTE #4-5 (Vol. 2)
95. RID #4-5 (Vol. 1)
96. Spotlight – Trailcutter(Trailbreaker renamed)
97. Spotlight – Hoist
98. More Than Meets the Eye #6 (Vol. 2)
99. More Than Meets the Eye Annual 2012 (Vol. 3)
100. More Than Meets the Eye #7-8 (Vol. 2)
101. Robots in Disguise #6-10 (Vol. 2, 3)
102. More Than Meets the Eye #9-13 (Vol. 3, 4) and text story “A Signal To Noise” (Vol. 4)
103. Robots in Disguise Annual 2012 (Vol. 3)
104. Robots in Disguise #11-16 (Vol. 3, 4)
105. More Than Meets the Eye #14-15 (Vol. 4)
106. Robots in Disguise #17-20 (Vol.5)
107. More Than Meets the Eye #16-21 (Vol. 4, 5) and text story “The Sound Of Breaking Glass” (Vol. 5)
108. Robots in Disguise #21-22 (Vol. 5)
109. More Than Meets the Eye #22 (Vol. 5)
VII. Dark Cybertron110. Dark Cybertron (Voll. 1-2)
VIII. Dawn of the Autobots111. Robots in Disguise #28
112. More Than Meets the Eye #28
113. Windblade #1