If you prefer full level playthroughs then these videos cover every secret, elite guard, field drone, rune, codex, and challenge in the game:
The UAC (level 1)Codex (1/2) - 0:00:16
Secret (1/3) - Collectible 1 (Classicguy) - 0:02:24
Automap - 0:03:06
Elite Guard (1/1) - 0:03:33
Secret (2/3) - Secret door level - 0:04:40
Codex (2/2) - 0:05:48
Field Drone (1/1) - 0:06:05
Secret (3/3) - Collectible 2 (Blueguy) - 0:07:32
Resource Operations (Level 2)Secret (1/8): 0:00:50
Automap: 0:01:25
Secret (2/8) - Secret door lever: 0:02:20
Codex (1/2): 0:04:18
Field Drone (1/1): 0:08:17
Secret (3/8) - Elite Guard (1/3): 0:09:23
Secret (4/8) with Plasma Rifle: 0:10:10
Secret (5/8) leads to Secret (6/8) - Elite Guard (2/3): 0:10:48
Secret (7/8) - Collectible (Doomguy): 0:13:37
Codex (2/2): 0:15:45
Elite Guard (3/3): 0:16:26
Secret (8/8) - Collectible (Bronzeguy): 0:17:19
Argent Cell (1/1): 0:17:37
Foundry (Level 3)Field Drone (1/1): 0:00:00
Codex (1/3): 0:00:00
Elite Guard (1/3): 0:00:39
Secret (1/6): 0:00:58
Secret (2/6) - Collectible (Vaultguy): 0:02:56
Three Possessed, One Barrel Challenge: 0:04:14
Codex (2/3): 0:04:33
Secret (3/6) with Rocket Launcher: 0:04:40
Curb Stomp Challenge: 0:05:29
Secret door lever: 0:06:29
Secret (4/6) - Secret door: 0:07:16
Argent cell (1/1): 0:08:22
Codex (3/3): 0:09:03
Secret (5/6) - Collectible (Prototypeguy): 0:09:19
Secret (6/6) - Elite Guard (2/3): 0:10:04
AutoMap: 0:11:00
Elite Guard (3/3): 0:15:09
Argent Facility (Level 4)Rune (1/2): 0:00:12
Codex (1/4) and Secret (1/5) - Secret door lever: 0:01:19
Elite Guard (1/4): 0:02:50
Codex (2/4): 0:04:37
Argent Cell (1/1): 0:05:18
Secret (2/5) - Collectible (UACguy): 0:06:32
Rune (2/2): 0:07:04
Secret (3/5) with Super Shotgun: 0:09:39
Codex (3/4): 0:11:48
Secret (4/5) - AutoMap: 0:13:01
Elite Guard (2/4): 0:13:29
Field Drone (1/2): 0:14:13
Elite Guard (3/4): 0:14:52
Secret (5/5) - Collectible (Stealthguy): 0:15:35
Codex (4/4) and Field Drone (2/2): 0:16:29
Elite Guard (4/4): 0:18:39
Argent Energy Tower (Level 5)Codex (1/4): 0:00:53
Rune (1/2): 0:01:09
Secret (1/7) - Argent Cell (1/2): 0:02:32
Chiropractor challenge pt 1: 0:03:36
Secret (2/7) - Field Drone (1/1) and Codex (2/4): 0:05:24
Secret (3/7) - Elite Guard (1/3): 0:07:28
Codex (3/4) and AutoMap: 0:08:19
Chiropractor challenge pt 2: 0:08:55
Over Killer challenge pt1: 0:09:05
Elite Guard (2/3): 0:10:05
Codex (4/4): 0:10:20
Secret (4/7) - Collectible (Orangeguy): 0:10:26
Over Killer challenge pt 2: 0:11:30
Secret (5/7) - Collectible (Purpleguy): 0:13:07
Argent Cell (2/2): 0:15:54
Secret (6/7) - Secret lever and door: 0:16:28
Rune (2/2): 0:20:55
Elite Guard (3/3): 0:22:30
Secret (7/7) with Gauss Cannon: 0:23:16
Kadingir Sanctum (Level 6)Secret (1/6): 0:00:17
Codex (1/7) and Elite Guard (1/4): 0:03:50
An example of Sweep the Leg challenge: 0:05:37
Secret (2/6) - Collectible (Astroguy): 0:06:24
Secret (3/6) - Rune (1/2): 0:08:58
Argent Cell (1/1): 0:10:09
Secret (4/6) with Chaingun: 0:11:09
Elite Guard (2/4): 0:12:15
Rune (2/2): 0:14:54
AutoMap: 0:16:01
Secret (5/6) - Collectible (Redguy): 0:16:20
Elite Guard (3/4): 0:16:40
Codex (2/7): 0:16:53
Codex (3/7): 0:16:58
Codex (4/7) and Field Drone (1/1): 0:17:17
Secret (6/6) - Secret Lever and Door: 0:19:46
Codex (5/7): 0:21:57
Codex (6/7): 0:22:54
Elite Guard (4/4): 0:23:07
Codex (7/7): 0:23:47
Argent Facility (Destroyed) (Level 7)Codex (1/5): 0:00:00
Secret (1/6) - Secret Lever and Door: 0:00:23
Secret (2/6) - Collectible (Rageguy): 0:01:03
Elite Guard (1/4): 0:01:30
Codex (2/5): 0:01:49
Rune (1/2): 0:04:47
Secret (3/6) - Elite Guard (2/4): 0:05:53
AutoMap: 0:08:03
Codex (3/5): 0:08:10
Elite Guard (3/4): 0:09:27
Codex (4/5): 0:11:23
Secret (4/6) - Field Drone (1/1): 0:13:14
Rune (2/2): 0:13:52
Argent Cell (1/1): 0:16:09
Codex (5/5): 0:17:50
Secret (6/6) - Collectible (Patriotguy): 0:18:08
Elite Guard (4/4): 0:18:33
Advanced Research Complex (Level 8)Secret (1/10) - Elite Guard (1/3) and AutoMap: 0:00:08
Bottle Opener Challenge: 0:00:55
Argent Cell (1/2): 0:01:10
Codex (1/4): 0:01:50
Codex (2/4): 0:04:58
Elite Guard (2/3): 0:05:11
Secret (2/10) - Rune (1/2): 0:06:42
Secret (3/10) with Mega-Health: 0:08:23
Secret (4/10) - Collectible (Phobosguy): 0:08:45
Secret (5/10) - Secret Lever and Door: 0:09:05
Secret (6/10) - Argent Cell (2/2): 0:10:04
Secret (7/10) - Field Drone (1/1): 0:10:54
Secret (8/10) - Elite Guard (3/3): 0:11:47
Codex (3/4): 0:12:35
Secret (9/10) - Collectible (Pinkguy): 0:12:49
Codex (4/4): 0:13:25
BFG: 0:14:01
Secret (10/10) - Rune (2/2): 0:15:25
Lazarus Labs (Level 9)Codex (1/5) leads into Siphon Grenade: 0:00:00
Secret (1/9): 0:01:03
Secret (2/9) - Elite Guard (1/4) and Codex (2/5): 0:03:30
Field Drone (1/1): 0:04:05
AutoMap: 0:04:28
Codex (3/5): 0:04:45
Secret (3/9) - Rune (1/2): 0:05:00
Secret (4/9) - Elite Guard (2/4): 0:09:53
Secret (5/9) - Collectible (Eliteguy): 0:12:00
Secret (6/9) - Collectible (Toxicguy): 0:12:36
Codex (4/5) and Argent Cell (1/1) and Time Well Spent challenge: 0:12:51
Secret (7/9) + (8/9) - Elite Guard (3/4) - Lever and Secret Door: 0:16:20
Secret (9/9) - Elite Guard (4/4) and Rune (2/2): 0:19:10
Thread the Needle Challenge: 0:20:29
Codex (5/5): 0:22:55
Titan's Realm (Level 10)Codex (1/4): 0:00:04
Secret (1/6) - Elite Guard (1/2): 0:01:09
Secret (2/6) - Field Drone (1/1): 0:03:16
Dominator challenge part 1: 0:03:49
Dominator challenge part 2: 0:05:26
Atop the Mountain challenge: 0:07:50
Secret (3/6) - Collectible (Keenguy): 0:08:36
AutoMap: 0:08:50
Secret (4/6) - Collectible (Silverguy): 0:09:30
Dominator challenge part 3 and Elite Guard (2/2): 0:10:28
Argent Cell (1/1) and Codex (2/4): 0:11:19
Secret (5/6) - Secret Lever and Door: 0:14:00
Trick Shot challenge: 0:15:55
Codex (3/4): 0:17:20
Secret (6/6): 0:17:30
Codex (4/4): 0:18:41
The Necropolis (Level 11)Codex (1/3): 0:00:05
Wait For It Challenge Part 1: 0:00:10
Wait For It Challenge Part 2: 0:00:55
Wait For It Challenge Part 3: 0:01:58
A Pin Pops a Balloon Challenge (equip Dazed and Confused rune): 0:03:45
Secret (1/3) - Lever and Secret Door, AutoMap, Codex (2/3) and Argent Cell (1/1): 0:04:10
Codex (3/3): 0:10:05
Two Mouths to Feed Challenge: 0:10:25
Secret (2/3) - Collectible (Tealguy): 0:10:35
Elite Guard (1/2): 0:10:55
Field Drone (1/1): 0:11:12
Elite Guard (2/2): 0:14:20
Secret (3/3) - Collectible (Hazmatguy): 0:15:30
VEGA Central Processing (Level 12)Codex (1/4): 0.00.04
Elite Guard (1/3): 0:00:28
Secret (1/5) - Collectible (Quakeguy): 0:00:49
Variety is the Spice of Death Challenge: 0:01:05
Gore Pinata Challenge: 0:05:25
Codex (2/4): 0:06:24
AutoMap leads to Secret (2/5) - Elite Guard (2/3) leads to Secret (3/5) - Lever and Secret Door: 0:06:36
Secret (4/5) - Collectible (Jungleguy): 0:08:26
Codex (3/4): 0:08:54
Secret (5/5) - Elite Guard (3/3): 0:16:39
Codex (4/4): 0:17:40
Argent D'Nur (Level 13)Big [Redacted] Gun Challenge Part 1: 0:00:25
Secret (1/5): 0:02:48
Big [Redacted] Gun Challenge Part 2: 0:03:27
AutoMap: 0:04:27
Big [Redacted] Gun Challenge Part 3: 0:05:52
Secret (2/5) leads to Secret (3/5) - Lever and Secret Door: 0:07:55
Secret (4/5) - Collectible (Cosmoguy): 0:12:15
Secret (5/5): 0:12:57
Hold Still Challenge: 0:16:30
Collectible (Goldguy) - Defeat final boss: 0:18:10