Spoilers below. If you're playing the game for the first time, please refrain from looking at these.
Back when PokéUE was still on Game Jolt, it had trophies for finding the easter eggs:
D'aww: The Pikachu loves you!
Let It Go: Let it go, let it go, turn away and slam the door, I don't care what they're going to say. Let the storm rage on; the cold never bothered me anyway.
Ghost Ship: Who turned the lights off?
Playtime Is Ogre: find the "A Cold Night" story
Pervert: Talk to Erika or Sabrina while wearing the Nude "Outfit".
Thief: Steal the last Pokéball from Oak's lab.
Undermon
I think they could serve as good hints. :)
And as for the legendaries, there are a lot:
Celebi: I think Celebi was a 0.3 exclusive Pokémon. It might be available in a Mystery Gift. I don't remember... You can obtain it by holding a GS Ball and interacting with a statue in the Forest Ruins (I think that's what the place was called, it's been a long time...). If you're using Debug mode, you can add GS Ball into your inventory.
Regice: Seafoam Islands
Regirock: Victory Road
Registeel: Moonside Lake
Regigigas: Mt. Moon
Ho-Oh: South Amber Road
Lugia: The Dead End (I think...)
Articuno (Roaming, more info below)
Zapdos (Roaming, more info below)
Moltres (Roaming, more info below)
Latias: Trainer Tower
Latios: Trainer Tower
Cobalion: I don't remember, sorry
Terrakion: I don't remember, sorry
Virizion: I don't remember, sorry
Keldeo: I don't remember, sorry
Entei (Roaming, more info below)
Raikou (Roaming, more info below)
Suicune (Roaming, more info below)
Deoxys: I don't remember, sorry (An exclusive item may be required)
Mew: I don't remember, sorry (An exclusive item may be required)
Mewtwo: I don't remember, sorry (An exclusive item may be required)
Arceus: Mallet Town :)
Roaming Pokémon
RUNKO:
Pokémon start roaming after the champion is defeated
Articuno:
(Western Runko)
Route 18 -> Route 19
Route 19 -> Sea Route 20
Sea Route 20 -> Route 21 or Sea Route 22
Sea Route 22 -> The Dead End or Sea Route 20
The Dead End -> Sea Route 22
Route 21 -> Runko Harbor
Runko Harbor -> Route 18
Zapdos:
(Central Runko)
Route 2 -> Route 3
Route 3 -> Fucksia Woods
Fucksia Woods -> Route 8
Route 8 -> Route 14 or Route 3
Route 14 -> Route 15
Route 15 -> Route 16
Route 16 -> Route 17
Route 17 -> Route 2
Moltres:
(Eastern Runko)
Route 4 -> Route 5
Route 5 -> Route 6
Route 6 -> Route 23 or Route 7
Route 23 -> Route 6
Route 7 -> Route 11
Route 11 -> Route 9
Route 9 -> Route 4
RUNKKU ISLANDS:
Pokémon start roaming after Final Cave is cleared
Entei:
(Western Runkku Islands)
Chroma Road -> Chroma Cave or Indigo Path
Chroma Cave -> Chroma Road
Indigo Path -> Victory Road (Outside) or Victory Road (Cave 1) or Victory Road (Cave 2)
Victory Road (Outside) -> Victory Road (Cave 1) or Victory Road (Cave 2) or Chroma Road
Victory Road (Cave 1) -> Victory Road (Outside) or Victory Road (Cave 2)
Victory Road (Cave 2) -> Victory Road (Outside) or Victory Road (Cave 1)
Suicune:
(Central Runkku Islands)
South Amber Route
North Amber Route
Moonside Lake
East Amber Route
(Moves through these four at random)
Raikou:
(Eastern Runkku Islands)
Morass Island
East Amber Route
Northern Plateau
Northern Cliffside
(Moves through these four at random)
Hope these will help you completionists!