GOTY map files seem to be *earlier* then the beta files. With the ones in the original release 1.002f being later, and the ones in GOTY 1.110 being the latest.
Those latest files are the source for Deus Ex Maps patch, distrubuted untouched.
Beta has correct computer codes, more details, more datacubes available, more pathing then GOTY

DeusEx.u (Gameplay)
Stealth pistol can have recoil mods in the beta Even though both versions have 0.1 recoil
Looks like the legend menu for playing music was more crude
Displayed for example "HKClub2_Music" instead of "Hong Kong Club 2"
Plasma is... different
That's weird, I wouldn't have expected a Level.Netmode check before multiplayer
Hey, if you can get beta to work with DeusEx.u, check out plasma for me, it's different
Something to do with its trail
Looks like there's a glitch during the end of the game where the game fades out while credits are playing
Looks like there's also a glitch in the beta where the game would only count you as killing the terrorists outside Osgood's if you hadn't killed them, or if you knocked them out, but not if you actually killed them
HKChair had a bad sitpoint
FireExtinguishers probably relied on the halon gas to extinguish the player, instead of it extinguishing you 100% of the time on use
Placing grenades on walls didn't update the text amount of grenades on your belt
I think items on bodies would always be deleted while in the final version it's only deleted if you have a copy of the item in your inventory
Synthetic Heart might not work properly in beta too, not sure
The player isn't extinguished on level transitions, that apparently breaks stuff, probably if you go back to the level where you were on fire you catch fire again
Running out of energy does something different, I think it either puts the message in your log or in your notes for some reason
I think the end game cinematic isn't skippable
Hmm, Unreal style dodging might be possible by default too
And that's pretty much it

CoreTexDetail.utx (Textures)
Diferent Gamma values.
Only one texture is the same

01_NYC_UNATCOHQ
One datacube is different "UNATCO and the Future"
Exactly the same except final has the addition of "[Document filtered per UNATCO Terror Monitoring Act 919-05 Sec. IV]"

02_NYC_Street.dx
UNATCO troops outside the Ton that give gas grenades are broken in the beta. Talking to the one on the right makes the one on the left talk

02_NYC_BatteryPark
Subway hostages are broken in the beta. Conversation always forces the male hostage to talk, if he's dead then you can't tell the female one to escape

03_NYC_UNATCOHQ
SamCarter has no reactions to 03 UNATCO beta
More pathing for him in the beta

03_NYC_BatteryPark
m03meet filben has a changed JC line, inflection is different betalink finallink
Subway hostages are broken in the beta. Conversation always forces the male hostage to talk, if he's dead then you can't tell the female one to escape

03_NYC_747
The conversation with Lebedev is different. I think the audio is the same, but I don't know how it plays out in game, the events have been shuffled a bit in the .con file

04_NYC_Street
Jock's line as he drops you off is different.
"Your brother's hurt pretty bad.  You'll find him at the apartment.  If he can walk, get him to come with you.  I can pick you guys up in Battery Park."
vs
"Your brother's hurt pretty bad.  You'll find him at the apartment."
Not just cut, different recording.

05_NYC_UNATCOMJ12lab
Conversation with Paul is different, has additional lines from a doctor. Tags are still in final

06_HongKong_WanChai_Street
In all versions there's a 50 skillpoint bonus under Jock's apartment, don't think it's possible to get without glitches

06_HongKong_MJ12lab
MIB voices are modified

12_Vandenberg_???
MIB Chatter is lacking the voice effect.
Various audio is lacking radio static

15_Area51_Entrance
MIB Hangar barks are modified.

15_Area51_Page:
An invisible collision mover that blocks the computer in the Aquinas router To prevent you from using it through the doors that lock it
There's a dead scientist with a datacube on a roof

15_Area51_Final
There's events to make the big door that flies at you make sounds when it lands (double check that this isn't in a51page)
Removed hidepoints, might be because the human pawns can't get to them
Extra pathing in some areas in beta
Gray's room has a keypad in it Code is 31729 in beta, 4167 in final
Beta: UserList(0)=(Username="Lab 12",Password="graytest")
Final: UserList(0)=(Username="graytest",Password="Lab12")
CoolantCut -> coolantcut (what is the exact context of this?)
I think that the biggest different in A51 Final is just going to be that the mover creation areas are there in beta
Beta doesn't have 3 logic triggers in it(Context?)

Misc:
Beta doesn't have UNATCOBarks con files,same as GOTY
DeusExDanceMix_Music.umx : Looks like he added effects to control tempo and ticks in the final version
In the credits Alexander Brandon isn't credited for Jimmy, typo in Kimberli Daniels' credit, Kris Nevins is credited as Jimmy instead (no other credits, not mentioned in final credits, probably brother of Will Nevins who does a few voices)