This includes as many items as possible - including PokeDex and Journal (that stuff)
I will also put (PT) or (D/P) next to the items IF they are only for One or Two Versions, and not the others - if there is not a (PT) or (D/P) next to it, it is available in all versions.
HMs given by NPCs
Cut: Cynthia gives it to you in Eterna city after you beat Gardenia.
Surf: Cynthia's Grandma gives it to you in Celestic town.
Strength: When you go to Iron Island a lady who is blocking the cave gives it you.
Rock Smash: A hiker in a cave in Oreborough city gives it too you after you beat Roark.
Waterfall: Jasmine gives it to you in Sunnyshore city after you beat Volkner.
TMs given by Gym Leaders after defeating them
TM76 (Stealth Rock): - Roark, Orgeburgh Gym
TM86 (Grass Knot) - Gardenia, Eterna Gym
TM60 (Drain Punch) - Maylene, Veilstone Gym
TM55 (Brine) - Crasher Wake, Pastoria Gym
TM65 (Shadow Claw) - Fantina, Hearthome Gym
TM91 (Flash Cannon) - Byron, Canalave Gym
TM72 (Avalanche) - Candice, Snowpoint Gym
TM57 (Charge Beam) - Volkner, Sunyshore Gym
Running Shoes: Player's mum.
Journal: Player's mum after returning from Sandgem
Parcel: Obtained from rival's mother in player's house, to deliver to rival
TM27 (Return): Obtained from Professor Rowan after leaving his Research Lab (Pt)
Pokédex: Obtained from Professor Rowan in the Pokémon Research Lab
National Pokédex: Upgraded by Professor Oak in the Pokémon Research Lab after
the player defeats the League and sees all Pokémon in the Sinnoh Region
Poké Radar: Obtained from Professor Rowan after Oak gives you the National Pokédex
Quick Claw: Obtained from girl on ground floor of Jubilife Condominiums
TM10 (Hidden Power): Obtained after defeating School Kids in Trainers School (D/P)
Potion: Obtained after defeating School Kids in Trainers' School (Pt)
Town Map: Obtained from rival after delivering the Parcel to him
Old Rod: Obtained from fisherman in gate
Fashion Case: Obtained from a Jubilife TV employee after defeating two Galactic Grunts
Vs. Recorder: Obtained from Looker on arrival (Pt)
Coupons 1, 2, and 3;
1. From Clown located between Poké Mart and Pokémon Center
2. From Clown located in front of the Pokétch Company headquarters
3. From Clown located in front of the Jubilife TV Station
Pokémon Watch: Obtained from inventor of the Pokétch after handing him all three coupons.
Memo Pad: Obtained from the Pokétch Company president after obtaining the Coal Badge.
Marking Map: Obtained from the Pokétch Company president after obtaining three Badges.
Link Searcher: Obtained from the Pokétch Company president after obtaining five Badges.
Move Tester: Obtained from the Pokétch Company president after obtaining Icicle Badge.
Heal Ball: Obtained in the house to the left of the Poké Mart, from a man on the second floor if shown a Zubat (In D/P) or Geodude (In Pt)
Great Ball: Obtained in the house below the Museum and to the right of the Pokémon Center, from a boy on the second floor
Dusk Ball: Obtained from a girl on the second floor of the northwestern-most building
Super Potion: Obtained from a worker in the bottom right corner of the town by the Mine entrance
Oran Berry: An Abra named Kazza is holding it.
TM88 (Pluck): From a girl in the house to the left of the flower shop
Random Berry: From a woman inside the flower shop (daily)
Sprayduck: From a woman inside the flower shop
Gracidea: From a woman on the vertical dirt path, requires fateful encounter Shaymin in the party (Pt)
Friendship Checker: Obtained from a woman in the Pokémon Center
Explorer Kit: Obtained from the Underground Man in the house next to the Pokémon Center
TM67 (Recycle): Received from the old lady in the Eterna Condominiums
Bicycle: A thank you from Rad Rickshaw for saving him from Team Galactic
Up-Grade: Given by Professor Oak after obtaining the National Pokédex (D/P)
Leppa Berry: Given by Charap, a Chatot
Shell Bell: Given by a woman in the Pokémon Hotel
Glitter Powder: Given by Keira in the Super Contest Hall
Tuxedo/Dress: Given by Johanna in the Super Contest Hall
Poffin Case: Given by the Fan Club Chairman in the Pokémon Fan Club
Day Care Checker: Man in the Pokémon Day Care
Pokémon History: Resident in the center of the town
Seal Case: Woman in the far eastern house
Alphabet Seals: Small boy in the far eastern house for showing the respective Unown
TM63 (Embargo): Man in the southern part of the city
Coin Case: Clown in a house, west of Veilstone Game Corner
Macho Brace: From the boy in the house north of the Poké Mart after showing him either all 3 forms of Burmy (In D/P) or a Male+Female Combee (In Pt)
Turtwig Mask: Accessory; obtained from a Parasol Lady near the Pokémon Center if the player started with Piplup (Chimchar Mask if started with Turtwig, Piplup Mask if started with Chimchar)
Random Berry: Woman in the SW-most house will give one of the move-weakening Berries (daily).
Great Ball: Man in the Pokémon Center if the first Pokémon in the player's party has high friendship
Choice Specs: From a man in the shop (during morning)
BlackGlasses : From a man in the shop (during day)
Wise Glasses: From a man in the shop (during night)
Analog Watch: From a Black Belt in the south-west house
TM48 (Skill Swap): In the first house upon entering from Route 218
Everstone: Held by a Haunter called Gaspar
Effort Ribbon: From a lady in the Sunyshore Market, if the player's Pokémon has 510 Effort values
Various Ribbons: Given by Julia, the lonely woman in the isolated house
Super Rod: From a Fisherman
Scope Lens: From the old lady in the Poké Mart
TM42 (Facade): From a man in the southernmost house
Potion: From Poké Mart employee.
Poké Ball ×5: Obtained from Dawn/Lucas after shown how to catch Pokemon.
TM78 (Captivate): Upper part; talk to the woman deep inside
Flag: From a girl in the southern gate
Exp. Share: From Dawn/Lucas's father in northern gate
Dowsing Machine: Obtained from Dawn/Lucas near Route 206 junction (D/P) or near entrance to Mount Coronet (Pt)
Vs. Seeker: Obtained from Dawn/Lucas near Route 206 junction (D/P) or near entrance to Mount Coronet (Pt)
Berry Searcher: Little girl in the Berry Master's house on the easternmost side of the route
Good Rod: Fisherman by Hearthome City entrance.
TM92 (Trick Room): A clown in the bungalow to the NW of the hotel entrance
Coin Toss app: Man inside a bungalow to the NE of the hotel entrance
Icicle Plate: Given by the Hiker in the house closest to HM08 after picking up HM08
Spell Tag: Given by woman in north house
Black Belt/Expert Belt/Focus Sash: Possible reward from the man in the house
TM56 (Fling): From the man near cliff edge
Fresh Water: Talk to the man in the house
Lum Berry: Magikarp named Foppa gives it to you
Nugget x2: Talk to man in the middle of the route. Keep talking to him for second one.
Feel free to comment if I missed something
Source: Bulbapedia, experience etc.