I'll be ordering everything by Generation the Pokemon was introduced. If they have a * next to it, it means it is still a signature move as of Gen 6
Gen 1
Frenzy Plant - Venusaur
Blast Burn - Charizard
Hydro Cannon - Blastoise
Skull Bash - Squirtle/Wartortle/Blastoise
Twineedle - Beedrill
Hyper Fang - Rattata/Raticate
Super Fang - Rattata/Raticate
Gust - Pidgey/Pidgeotto/Pidgeot
Glare- Ekans/Arbok
Petal Dance - Oddish/Gloom
Spore - Paras/Parasect
Volt Tackle - Raichu/Pikachu
Fissure - Diglett/Dugtrio
Payday - Mewoth/Persian
Extremespeed - Arcanine
Kinesis - Kadabra/Alakazam
Ally Switch - Kadabra/Alakazam
Low Kick - Machop/Machoke/Machamp
Vital Throw - Machop/Machoke/Machamp
Clamp - Shellder/Cloyster
Icicle Spear - Shellder
Night Shade - Gastly/Haunter/Gengar
Crabhammer- Krabby/Kingler
Barrage - Exeggcute/Exceggutor
Bone Club - Cubone/Marowak
Bonemerang - Cubone/Marowak
Hi Jump Kick - Hitmonlee
Jump Kick - Hitmonlee
Rolling Kick - Hitmonlee
Mega Kick - Hitmonlee
Mach Punch - Hitmonchan
Vacuum Wave - Hitmonchan
Softboiled - Chansey
Dizzy Punch - Kangaskhan
Waterfall - Goldeen/Seaking
Camouflage - Staryu
Substitute - Mr.Mime
Lovely Kiss - Jynx
Conversion - Porygon
Sharpen - Porygon
Conversion2 - Porygon
Sky Attack - Moltres
Ourage - Dratini/Dragonair/Dragonite
Psystrike - Mewtwo
Gen 2
Spider Web - Spinirak/Ariados
Volt Tackle - Pichu
Morning Son - Espeon
Pain Split - Misdreavus
Spikes - Pineco/Forretress
Metal Claw - Scizor
Megahorn - Heracross
Beat Up -Sneasel
Octazooka - Octillery
Present - Delibird
Steel Wing - Skarmory
Conversion - Porygon2
Conversion2 - Porygon2
Milk Drink - Miltank
Triple Kick - Hitmontop
Rolling Kick - Hitmontop
Sketch - Smeargle
Softboiled - Blissey
Aeroblast - Lugia
Sacred Fire - Ho-oh
Celebi - Hold Back*
Gen 3
Leaf Blade - Grovyle/Sceptile
Blaze Kick - Blaziken
Muddy Water - Marshtomp/Swampert
Extrasensory - Nuzlead
Slack Off - Slakoth/Slaking
SmellingSalt - Makuhita/Hariyama
Arm Thrust - Makuhita/Hariyama
Assist - Skitty
Signal Beam - Volbeat
Tail Glow - Volbeat
GrassWhistle - Roselia
Teeter Dance - Spinda
Needle Arm - Cacnea/Cacturne
Zangoose - Crush Claw
Poison Tail - Seviper
Weather Ball- Castform
Ice Ball - Spheal/Sealeo/Walrein
Mist Ball - Latias
Luster Purge - Latios
Doom Desire - Jirachi
Psycho Boost - Deoxys*
Gen 4
Defend Order - Vespiqueen
Heal Order - Vespiqueen
Attack Order - Vespiqueen
Chatter - Chatot
Rock Wrecker - Rhyperior
Conversion - Porygon-Z
Conversion2 - Porygon-Z
Roar Of Time - Dialga
Spacial Rend - Palkia
Magma Storm - Heatran
Crush Grip - Regigigas
Shadow Force - Giratina
Lunar Dance - Cresselia
Heart Swap - Manaphy
Dark Void - Darkrai
Seed Flare - Shaymin
Judgement - Arceus
Gen 5
Searing Shot - Victini
Heat Crash - Tepig/Pignite/Emboar
Secret Power - Audino
Storm Throw - Throh
Night Daze - Zorua/Zoroark
Tail Slap - Minccino/Cinccino
Skill Swap - Solosis/Duosion/Reuniclus
Horn Leech - Sawsbuck
Electroweb - Joltik/Galvantula
Gear Grind - Klink/Klang/Klinklang
Shift Gear - Klink/Klang/Kilnklang
Head Charge - Bouffalant
Fiery Dance - Volcarona
Sacred Sword - Cobalion / Terrakion / Virizion
Fusion Flare - Reshiram
Blue Flare - Reshiram
Fusion Bolt - Zekrom
Bolt Strike - Zekrom
Glaciate - Kyrurem
Fusion Flare - Kyurem-W
Ice Burn - Kyurem-w
Fusion Bolt - Kyurem-B
Freeze Shock - Kyurem-B
Secret Sword - Keldeo
Sacred Sword - Keldeo
Relic Song - Meloeta
Techno Blast - Genesect
Gen 6 (All of these still count, cbf to put a *)
Spiky Shield - Chesnaught
Mystic Fire - Delphox
Water Shruiken - Greninja
Mat Block - Greninja
Powder - Vivillion
Noble Roar - Litleo/Pyroar
Parting Shot - Pancham/Pangoro
King's Shield - Aegislash
Aromatic Mist - Aromatisse
Topsy Turvey - Inkay/Malamar
Happy Hour - Inkay
Electrify - Helioptile/Heliolisk
Flying Press - Hawlucha
Crafty Shield - Klefki
Fairy Lock - Klefki
Forest's Curse - Phantump/Trevanent
Trick-or-Treat - Pumpkaboo/Gourgeist
Geomancy - Xerneas
Oblivion Wing - Yveltal
Land's Wrath - Zygarde
Diamond Storm - Diancie
Source: Bulbapedia