On some Marathon maps, Bungie added annotations (or notes) to describe certain areas of the map. They can only be seen in map view or when the map is opened in a map editor.

A full list of these annotations has never been compiled until now. Thanks to poenadare <mstorysclm@mlcsmith.com> on the Story forum who has been systematically documenting these.

0. Arrival

Hanger 7A (Port)
Observation Deck #221

Notes
Hanger 7A (Port) was the answer to 25th question in the Seventh HoTBob Competition.

1. Bigger Guns Nearby

BioCore Vent #88A
BioCore Vent #88B

2. Never Burn Money

AMS Tower
Deprivation Chamber

Notes:
AMS stands for Automatic Manufacturing Systems. In the terminals this section of the map is called the Manufacturing Transport Station.

3. Defend THIS!

*none*

4. Couch Fishing

*none*

5. The Rose

Recreation Area #5
Fun House
The Stem
Stamen
Pistil

Notes
Petals is an annotation on The Rose which can be viewed with a map editor but it does not display in map view. Why? Well on the Story forum treellama <wolfy@treellama.org> explained the mystery of the missing map notation. He wrote:

I hacked Weland to print out the polygons associated with annotations, and opened
up the M1A1 version. That annotation is associated with polygon 148, which is the
most southernly tine of the "Fun House" fork. So, unless you have that on your
automap you won't see the "Petals" annotation.

Unfortunately if you try to display both the 'Fun House' and the 'Petals' section of the Rose in
map view you lose the map annotations. The level is just too big. Hence you will never see it.

6. Smells Like Napalm, Tastes Like Chicken

Tunnel System #B972AF
Shuttle Drydock
Tunnel System #A894C

7. Cool Fusion

Experimental Vacuum Chamber
Charge Conduit (North)
The Wave
Lift #A7

8. G4 Sunbathing

#41-a
Airlock 2
Airlock 5
M.C. Control
D.S. Control
D.V. Control
Dead Sea
Death Valley
Satellite Relay

Notes
Death Valley and Dead Sea were not the original annotations. Using a map editor you can see remnants of the original names, namely:

Dead Seaa Landing
Death Valleynding

Both seem to have ended with the word 'Landing'. Since this is G4 Sunbathing Landing Station it would make sense.

9. Blaspheme Quarantine

Q1
Q2
Q3
Q4
Quarantine Center
Quarantine Storage

10. Bob-B-Q

*none*

11. Shake Before Using...

*none*

12. Fire! Fire! Fire! Fire! Fire!

*none*

13. Colony Ship For Sale, Cheap

*none*

14. Habe Quiddam

*none*

15. Neither High nor Low

Core Center

16. Pfhor Your Eyes Only...

*none*

17. No Artificial Colors

*none*

18. Unpfhorgiven

*none*

19. Two Times Two Equals...

*none*

20. Beware of Low-Flying Defense Drones...

*none*

21. Eupfhoria

*none*

22. Pfhoraphobia

*none*

23. Ain't Got Time Pfhor This...

*none*

24. Welcome to the Revolution......

Cargo A
Cargo B
Cargo C1
Cargo C2

25. Try again

Engineering Storage
Fusion Vent #9

26. Ingue Ferroque

*none*

27. Mars Needs Women

The Coffin
Skylight
The Shaft
The Other Shaft

None of the other Marathon 1 net levels have annotations.

Map annotations in Marathon 2?

treellama <wolfy@treellama.org> in a Story forum post points out that the Marathon 2 net level 'Flight of the Toolator' has annotations, sixteen in total. They are listed below:

34. Flight of the Toolator

Teleporter #1
Dest. #1
Teleporter #2
Dest. #2
Teleporter #3
Dest. #3
Teleporter #4
Dest. #4
Teleporter #5
Dest. #5
Teleporter #6
Dest. #6
Teleporter #7
Dest. #7
Teleporter #8
Dest. #8

This is what Greg Kirkpatrick had to say about his level on the Level Credits section:

This map was made for Marathon but it never translated very well. In Marathon you could fly around with the flamethrower. Since that didn't work in Marathon 2 the map never really recovered.

Given that this map was ported over to M2 from M1 it might explain the presence of annotations since they do not appear to feature in maps made specifically for M2.

In the so-called 'beta' version of Marathon, that circulated on the net around October 1994, the level 'Mars Needs Women' was originally called 'Mars Wants Women'. This level contained annotations that were later removed from the demo and full game versions of 'Mars Needs Women'. The annotations on 'Mars Wants Women' are listed below:

0. Mars Wants Women

The Coffin
The Shaft
The Other Shaft
Carnage Central
Green Room

Confused? Well here is the 'beta' level, as viewed in an early version of Pfhorte. Carnage Central is the large room in the center of the map and Green Room is... well the Green Room (obvious when you see it).

Why Carnage Central and Green Room were removed and Skylight added to the demo and full game is not clear. Both annotations are self-explanatory and quite appropriate. Indeed, the area called Carnage Central continued to be referred to as this in the Marathon FAQ after the Marathon demo was released.