After many, many plays, I've found myself completing the quest for Doctor Matt that requires more that the 50%?-70%? of the city explored. Over time, my exploration percentage has risen from the original 52% on my first build, to the 90% on my final build. Since there's some things that will prevent me to reach the 100%, those are too few to make the 10%, so I've decided to put here a list of all locations that I've found, as well as my ways of finding them.
Primary Rooms
Grey Abbey Library: Default
Outside Trevor Labs: Hunt Trevor Labs
Capitol District
Approaching the Capitol Building: Hunt Capitol
Disused Garage: Hunt "Garage Demon" (Capitol)
Office Den: Hunt "Wolfrape" (Capitol)
Orc Lair: Escaping After "Orc Raid" (Warehouse). Locked out if you have Dominant feat
Central City
Camp Bravo: Hunt "Trickster Masterpiece", then "Back at the Camp"
Green Apartment: Hunt Green
Fire Station 86: Hunt Fire Station
Mini-Lab: Hunt "Another Researcher". After rescuing or abandoning Sam, the location will be unavailable.
Pediatrics Lobby: Hunt Pediatrics
Police Station: Submitting to Alexandra succesfully in the Doberman monster encounter (Charisma check)
Red Apartment: Hunt Red
Tyr's Club: After completing "DogHouse" (Warehouse) during Kenaz quest
City Park
Park Entrance: Hunt Park
Equinoid Camp: After recruiting Liliana as a pet (Park). If you have the Wereraptor curse, you've locked out of this location, so don't get close until you find the cure.
Lion's Den: Hunt "Feline Friend" (Park)
Commercial District
Smith Haven Mall: Hunt Mall
Back Alley: After talking to the Dragoness (Isolated Street), hunt "Another Ladder" (Mall Sewers)
Comic Shop: Hunt "Mephitness" (High Rise District)
Isolated Street: Hunt "Isolated Building" (Mall Sewers)
K9-Vans: Hunt "Canine Patrol" (Light Red District) three times
Kristen's Hideout: Hunt "Finding Kristen"
Lingerie Store: After rescuing Lance (Palomino) and starting his quest, or looking at the negligee given by the Butterfly (High Rise District)
New Ewe Store: Hunt "New Ewe Store", agreeing to help, hunt it again, then hunting "Little Lost Lamb"(Mall Sewers), then hunt again "New..."
The Palomino: Hunt "Dog Chase" between morning and evening, before reaching lvl5
Slutrat Den: Lose a fight against a Slut Rat (Mall Sewers) with a Rat body and remember the way back.
Dry Plains
Dry Plains: Hunt Dry Pains
McDermott Farm Entrance: Hunt "Missing Cow" (Dry Plains), choosing 1, then hunting it again
Researcher Studio: Hunt "For the Future" (Dry Plains)
Rocky Outcropping: Hunt "Peculiar Dragon" (Dry Plains)
Industrial Sector
Nutso Factory: Hunt "Finding Mack"(Warehouse) the second time during his quest
Plant Overwiew: Hunt Plant
Power Lines: Hunt Lines
Reservoir: Hunt Reservoir. Only after level 16. Currently not implemented.
Fair Grounds
State Fair: Hunt Fair
Sweet Tooth: Optionally finding first "Sweet Exchange" (Fair). Hunt "Sweet" (Fair)
High Rise District
Entrance to the High Rise District: Hunt High
Agency: Hunt "Informant" during Kenaz quest
Alex Condo: Hunt "Meet Alex" (High Rise District)
Bone-Appetit: Hunt "Gourmet Treats" (High Rise District)
Butterfly Grove: Hunt Butterfly (High Rise District) without forcing her, several times
Flower Garden: Hunt "Overrun Garden" (High Rise District), and defeating the Parasiting Plant.
Lizard Parlor: Finish "Friendship Proof"(Warehouse) first set of encounters, then the "Important Treasure"(Red Light District) during Omio questline, then the second half of "Friendship Proof"(Warehouse)
Rex's Place: Hunt "Forced Adoption", then using the toy thrice, then hunting again "Forced Adoption". If you choose to free Karen, the location won't be available after deling with Rex.
Zephyr Lobby: Default
Hospital
City Hospital: Hunt Hospital
Psych Department: Hunt "Another Doctor"(Hospital)
Junkyard
Abandoned lot: Hunt Abandoned lot
Hyena Shack: Hunt "Annoyed Hyena"(Junkyard)
Steven's Home: Hunt "Junkyard Home"(Junkyard) after sucessfully having sex with Steven
Misc
Foxy Hideaway: Finishing "Strange Fox" encounters, then hunt "Strange Bell" (Park), and finding "Strange Fox" a last time to return it.
Qytat Plaza: Hunt "Guard Gryphon", defeating the guard, then climbing the sky-staircase (Red Apartment/Green Apartment/Bright Alley)
Museum
Museum Foyer: Hunt Museum
Egypt Wing Entrance: Hunt "Wing"(Museum)
Light Red District
Entrance to the Red District: Hunt Light Red
Bradford's Camp: Hunt "Bounty Hunter"(Light Red)
Bright Alley: Hunt Bright
Burned-Out Chapel: Hunt Chapel, or "AngelvsDemons" (Light Red) Encounter
Cuero Lobo: Hunt "Leather Wolf" (Light Red)
Dow Under Pub: Hunt "Aussie Pub" (Light Red)
Gillian's Flat: After visiting the Pub several times (Nuber of visits needed yet to determine)
Police Car: Agreeing to help the police in "Police..." (High Rise), and giving him the 5 keys
Porn Store: Hunt "Mouse Taur" (Light Red) or Porn Store (Light Red)
Sven's Place: Hunt "Hidden Kitty" (Light Red)
Tattoo Parlor: Hunt "Finding Kara"(Light Red) at the end of Harold quest
Seaside
Beach Plaza: Hunt Beach
Bouncy Castle: After getting the boat for the pirate island, hunt "Snared vixen". Available only during said quest.
Pirate Island: Finding "noteinabottle"(Beach), talking to Rod, then finding "findingBoat"(Beac
Viking Ship: Defeating Sonya's father during "Chieftain Challenge"
The Stables
Stables Hotel: Hunt "Stabled Situation" two time. You'll require a soda and a pack of chips to get access during the second encounter
Tenvalle College
College Campus: Hunt College. A skill check for catching a ball could reduce your HP, so be wary.
Astroslide Field Lockeroom: Go to the Athletic walkway in the college, then go SW.
Campus Gym: Hunt "Working Out"(College)
Phi Iota Gamma: ???
Sports Area Lockerroom: Hunt "Barricaded Lockerrom"(College). Be ware to not trigger Eric's event if you're not prepared.
Urban Forest
Urban Forest: Hunt Urban Forest
Bunny House: Hunt "Easter Bunny"(U.Forest)
Happy Puppy Kennel: Hunt "Corrupted Kennel"(U.Forest) and follow Dominick inside
Warehouse District
Warehouse District: Hunt Warehouse
Mike's Home: Hunt "Walking Dog" three times, dont' attack Mike on the first even, and defeat the Leoparman on the third one. Procure having a medkit on you pack to get Xerxes/Helena soon.
Spider's Web: Surrendering to Aelias 5-6 times in a row.
Wolfman's Lair: Defeating Septus 6-7 times in a row, then hunting "Entrance to the Lair" in the Outside exploration.
Zoo
Zoo Entrance: Hunt Zoo.
Gator Den: Defeat once the Sewer Gator (Mall Sewers)
Tiger Der: During "Tigervstaur"(Zoo) encounter, side against the Tigertaur
No-No Locations
Hyena Hideout: Hunt "Gang" two times, and follow Gina to the Hideout.
Pig Pen: Ewwww.... Hunt "Hungry Piggy" if you are into...that...sort...of...things.
Paleontology Lobby: Accept Dr Utah offer and reject the cure on the Museum at the end of the Wereraptor Cure questline. Forces a permanent Wereraptor curse on you, which will be displeasing (I guess) for many players.
Reservoir: Hunt Reservoir when level is 17 or bigger. (Discontinued)
Shifting Lab: Shifting questline, after defeating to Ebon Dragators. Locks out all the mutation endings, so I'll have to pass on this one.
Stablemaster Office: At the end of the Stables Quest
Note: No location indicates that the event is found on the Outside exploration.
Note II: My memory doesn't remember the full hunting event in most cases, so I've only added the word that made it work for me. Be ware that the word may belong to another event.