I'll work on timestamps for each game soon enjoy this redo video.

Mega Man 1
00:00 Wily Machine 1

Mega Man 2
1:08 Alien

Mega Man 3
4:22 Gamma

Mega Man 4
6:44 Wily Capsule

Mega Man 5
7:58 Wily Machine 5
10:36 Wily Capsule 2

Mega Man 6
15:15 Wily Machine 6

Mega Man 7
17:06 Wily Machine 7
18:32 Wily Capsule

Mega Man 8
19:37 Wily Machine 8
21:11 Wily Capsule

Mega Man 9
22:14 Wily Machine 9

Mega Man 10
23:34 Wily Capsule Duo

Mega Man 11
24:48 Wily Machine V1
26:44 Wily Capsule V2

Mega Man & Bass
28:57 Wily Machine/Wily Capsule

Mega Man & Bass 2
31:33 Shadow Rockman

Mega Man GB
32:54 Wily Machine

Mega Man GB 2
33:35 Wily Machine

Mega Man GB 3
34:38 Wily Machine 3

Mega Man GB 4
35:21 Wily Iron Robo Golem

Mega Man GB 5
36:52 Sunstar

Mega Man The Wily Wars
37:50 Wily Machine Golem

Mega Man Game Gear
38:39 Wily Capsule

Mega Man Powered Up
39:06 Wily Tank Machine
40:17 Wily Flying Capsule

Mega Man The Power Battle
41:31 Wily Fighter Machine
42:18 Wily Escape Capsule

Mega Man The Power Fighters 2
44:15 Wily Skull Machine
46:12 Wily Escape Capsule

Mega Man Battle & Power Neo-Gen
46:29 Wily Machine Fighter/Skull
47:28 Wily Escape Capsule

Mega Man X
48:50 Velguarder (Boss Theme)
49:52 Sigma
50:32 Wolf Sigma

Mega Man X2
52:25 Neo Sigma
52:53 Sigma Virus

Mega Man X3
53:32 Sigma
55:27 Kaiser Sigma
58:00 Sigma Virus

Mega Man X4
1:00:14 Reaper Sigma
1:02:19 Earth Sigma & Gunner Sigma

Mega Man X5
1:03:52 Psycho Sigma
1:06:07 Final Sigma W

Mega Man X6
1:09:17 Broken Sigma
1:11:20 Hell Sigma

Mega Man X7
1:12:51 Sigma (Phase 1)
1:15:42 Sigma (Phase 2)

Mega Man X8
1:18:21 Devil Sigma
1:20:28 Lumine (Phase 1)
1:22:23 Lumine (Phase 2)

Mega Man X Maverick Hunter
1:25:11 Velguarder (Boss Theme)
1:26:53 Sigma
1:28:20 Wolf Sigma

Mega Man Xtreme
1:30:38 Sigma
1:31:42 Wolf Sigma

Mega Man Xtreme 2
1:32:11 Neo Sigma
1:32:55 Beast Sigma

Mega Man X Command Mission
1:33:33 Great Redips

Mega Man Legends
1:37:43 Mega Man Juno (Phase 1)
1:41:43 Mega Man Juno (Phase 2)

Mega Man Legends 2
1:44:52 Sera (Phase 1)
1:46:36 Sera (Phase 2)

Misadventures of Tron Bonne
1:48:45 The Colossus

Mega Man Battle Network
1:50:40 Life Virus

Mega Man Battle Network 2
1:52:21 Gospel

Mega Man Battle Network 3
1:53:53 Alpha

Mega Man Battle Network 4
1:55:50 Duo.EXE

Mega Man Battle Network 4.5
1:58:15 Bass.EXE

Mega Man Battle Network 5
1:59:54 Nebula Grey

Mega Man Battle Network 6
2:03:01 Gregar/Falzar

Mega Man Battle Transmission
2:04:48 Life Virus MK2

Mega Man Phantom of Network
2:09:13 Cache.EXE

Mega Man Legends of Network
2:10:47 Trojan Horse

Mega Man Zero
2:12:12 Copy X (Phase 1)
2:15:06 Seraph X (Phase 2)

Mega Man Zero 2
2:18:39 Elpizo (Phase 1)
2:21:15 Elpizo (Phase 2)

Mega Man Zero 3
2:24:38 Golden Omega (Phase 1)
2:25:54 Fusion Omega (Phase 2)
2:28:00 Omega Zero (Phase 3)

Mega Man Zero 4
2:30:08 Dr. Weil (Phase 1)
2:32:16 Dr. Weil (Phase 2)

Mega Man ZX
2:35:21 Serpent (Phase 1)
2:37:47 Serpent (Phase 2)

Mega Man ZX Advent
2:40:46 Albert (Phase 1)
2:44:08 Albert (Phase 2)

Mega Man Star Force
2:47:43 Andromeda

Mega Man Star Force 2
2:50:23 Le Mu

Mega Man Star Force 3
2:52:28 Crimson Dragon