DISCLAIMER:
As of right now, this guide is mostly complete. However, there are several triggers that have not been conclusively established and there still may be errors.
Only quests or encounters with time dependent triggers and significant impact are included in this guide. More expansive lists can be found elsewhere such as the Reddit thread below.
Progressing into the next act will impact just about every unfinished quest. Don't do it until you have done everything you can in your current act.

CREDIT:
Much of this information comes from my playthroughs of the game. However, the following were important sources in helping acquire more information and thus deserve credit:

The Baldurs Gate 3 Wiki - https://baldursgate3.wiki.fextralife.com/Baldur's+Gate+3+Wiki

u/Neville_Lynwood - https://www.reddit.com/r/BaldursGate3/comments/15q1o77/list_of_time_sensitive_quests/

HELP AND FEEDBACK:
Please comment below if you have noticed anything regarding this topic and have thoroughly tested it. Specific triggers that start and end the quest or encounter as well as alternative permutations are very helpful to know. If you have feedback for this guide, please comment below as well.

FORMAT:
Each entry will be formatted in this way:

Quest or Encounter Name
Description
ST: Start Trigger
ET: End Trigger

THANKS:
I also want to thank the community for the support and feedback I have received for my work on this guide!

COMPANION QUESTS

Gale is a Lil Hungry
Gale will tell you he needs to consume magic items or he will be forced to do some shady stuff
ST: Two long rests or his approval increases to "Fair"
ET: Gale stops asking after being fed three times, or, will resort to other methods after enough long rests

Karlach
Karlach will leave the party if you do not kill her pursuers
ST: Karlach joins party
ET: Unknown amount of long rests


WILDERNESS

True Souls Edowin, Andrick, and Brynna
Andrick and Brynna will be gone after a long rest
ST: Encounter triggered by proximity
ET: A long rest will eliminate encounter

Owlbear Momma
Owlbear mother will be killed by goblins if you did not kill it
ST: Owlbear cave is entered
ET: Owlbear is dead after a long rest


DRUID GROVE

Bugbear Assasin
The bugbear assassin will kill the Tiefling girl by telescope if you do not intervene
ST: Encounter is triggered by proximity
ET: Girl is killed after in-game timer

Investigate the Beach
Child Tiefling on the beach will die if you do not intervene
ST: Quest is initiated
ET: Child will die, trigger is unknown

Save Arabella
Kagha will kill Arabella
ST: Quest is initiated
ET: Child will die, trigger is unknown. Also killed after attacking goblin camp.

Save the Goblin Sazza
Sazza will die if you break out Halsin or attack the druid grove
ST: Initate quest
ET: Break out Halsin, or the attack on the druid grove begins

Druid Grove Ritual
The ritual will complete, the grove will be closed off, and the Tieflings will be driven out and die. The only certain way to stop it is to deal with Kagha.
ST: Entering the druid grove
ET: There are several triggers that will close the grove such as stealing the idol, killing tieflings, or entering the mountain pass or Grymforge. It appears long rests have no impact. See video link in comments for more info.

Raid the Druid Grove
The sequence that leads to the raid on the druid grove will trigger once you talk to Minthara in the Goblin Camp. Long resting after this will begin the encounter and quests inside the grove will be locked and unable to be completed.
ST: Initiate dialogue with Minthara
ET: A long rest


BLIGHTED VILLAGE:

The Gnome on the Windmill
The Gnome will disappear
ST: Proximity trigger
ET: Trigger is unknown


RISEN ROAD:

Find the Missing Shipment
The caravan guards will be killed by Kobolds if left for too long. Quest will still be completable
ST: Proximity Trigger
ET: The guards will die after a long rest

Rescue the Trapped Man & Rescue the Grand Duke
Everyone in the burning inn will die if not rescued
ST: Quest is initiated
ET: In-game timer


MOUNTAIN PASS:

Lae'Zel Confronts the Githyanki
Lae'Zel will die if she has left the party to talk to the patrol and you do not join her
ST: Lae'Zel leaves party
ET: Triggered if you leave the general area


UNDERDARK:

Cure the Poisoned Gnome
Thulla will die if not healed or given an antidote
ST: Initiate Quest
ET: Triggered by unknown amount of long rests or by completing the quest to deal with Nere


GRYMFORGE:

Free True Soul Nere
Nere and a few gnomes will die if you do not clear the rubble in time
ST: Quest is initiated
ET: In-game timer, or a long rest, or 2 camp visits

Shadow-Cursed Lands

Don't Let Rolan Die
Rolan will be found on by the southern most bridge in the Shadowfell after leaving the Last Light Inn. He will die if not saved from the shadows that attack him.
ST: Proximity trigger
ET: In-game timer

The Harpers Ambush Kar'niss
The ambush won't trigger properly if you delay too long after the harpers leave the Last Light Inn. This will result in being unable to obtain the moonlantern from Kar'niss
ST: Harpers leave for the ambush
ET: Unclear if long rest or in-game timer

Lift the Shadow Curse
You should play hide and seek with Oliver before Halsin rescues Thaniel from the Shadowfell. This will avoid bugs in this quest.
Halsin will die if you leave while he enters the Shadowfell
ST: Halsin enters the Shadowfell
ET: A long rest


Moonrise Towers

Rescue Wulbren & Rescue the Tieflings
You must rescue everyone in the prison by the time you complete the area, otherwise they will die
ST: Quests are initiated
ET: It appears that entering the Shadowfell to find the Nightsong is the trigger.

Companion Quests

Rescue Orin's Victim
A companion will be kidnapped by Orin and will be killed if you do not save them.
ST: Entering the sewers
ET: Unknown trigger or amount of long rests

Rivington

Help the Devilish Ox
The Strange Ox will disappear after some time if you have not agreed to help him
ST: Entering Rivington
ET: Unknown amount of long rests or entering the Lower City


Wyrm's Rock

Save Counsellor Florrick
Counsellor Florrick will be executed if you do not save her
ST: Unsure, possibly Gortash's coronation
ET: 5 long rests


Lower City:

Stop the Presses
Your reputation will be tarnished if you do not stop the Baldur's Mouth from publishing their story
ST: Quest is initiated
ET: A long rest (Reportedly changed to 2 long rests in Patch #5)

Investigate the Murders
Cora will be dead at the wine festival unless you warn her
ST: Quest is initiated, or potentially entering the lower city
ET: Unknown amount of long rests

Save Duke Ravengard
To rescue Duke Ravengard you must do the following sequence of events: Attend the Gortash coronation and do not kill Gortash, talk with Mizora and update the Wyll's pact after a long rest, then go to the Iron Throne prison.
The prison will be blown up by Gortash a number of turns after you dock. Be prepared to rescue the prisoners.
ST: Docking at the prison
ET: In-game combat, 5-8 turns