For those of you using the Joy-Con Toolkit from @CTCaer to customize your Nintendo Switch Joy-Con colors, and if you're in need of special colors to help you on your way, today's your lucky day my friend, for I, Patrick "TheWolfBunny" Adams, have gathered many color values to help you on your way for your adventures. I'll try to deliver as many as I can. The hex color value I 100% recommend that you use for the buttons is #0F0F0F (black), for my color values are all official colors that I've scanned, put a lot of effort into collecting all in a single document, specifically categorized, and are all yours to choose from. So, without further ado, pick whichever colors you like for your own personalized Joy-Cons. And I'll continue to update this thread with more colors for you to use.
Super Smash Bros. for Wii U
Smash Wii U P1 Red: #F52E2E
Smash Wii U P2 Blue: #5463FF
Smash Wii U P3 Yellow: #FFC717
Smash Wii U P4 Green: #1F9E40
Smash Wii U P5 Orange: #FF6619
Smash Wii U P6 Cyan: #24D4C4
Smash Wii U P7 Purple: #D41CE5
Smash Wii U P8 Slate: #4A4559
Smash Wii U CPU Gray: #616161
Smash Wii U E3 2014 P2 Blue: #5409FF
Super Smash Bros. for Nintendo 3DS
Smash 3DS P1 Red: #FF2021
Smash 3DS P2 Blue: #214DFF
Smash 3DS P3 Yellow: #DE8A00
Smash 3DS P4 Green: #089200
Smash 3DS CPU Gray: #848684
Super Smash Bros. Brawl
Brawl P1 Red: #FF0000
Brawl P2 Blue: #4753FF
Brawl P3 Yellow: #FFBB0F
Brawl P4 Green: #249F3F
Brawl CPU Gray: #909090
Super Smash Bros. Melee
Melee P1 Red: #F15959
Melee P2 Blue: #6565FE
Melee P3 Yellow: #FEBE3F
Melee P4 Green: #4CE44C
Melee CPU Gray: #7F7F7F
Super Smash Bros.
Smash 64 P1 Red: #ED3636
Smash 64 P2 Blue: #4E4EE9
Smash 64 P3 Yellow: #FDDF1A
Smash 64 P4 Green: #4EB94E
Smash 64 CPU Gray: #ACACAC
Rivals of Aether
P1 Red: #ED1C24
P2 Blue: #00B7EF
P3 Pink: #FFA3B1
P4 Green: #A8E61D
Indie Pogo
P1 Blue: #6383B8
P2 Red: #D93F60
P3 Green: #41BB5A
P4 Yellow: #E49937
(I actually got these colors from Lowe Bros. themselves to share with you!!!)
THE iDOLM@STER
Haruka Amami: #E22B30
Chihaya Kisaragi: #2743D2
Yukiho Hagiwara: #D3DDE9
Yayoi Takatsuki: #F39939
Ritsuko Akizuki: #01A860
Azusa Miura: #9238BE
Iori Minase: #FD99E1
Makoto Kikuchi: #515558
Ami and Mami Futami: #FFE43F
Miki Hoshii: #B4E04B
Takane Shijou: #A6126A
Hibiki Ganaha: #01ADB9
Kotori Otonashi: #FFF09F
765 Production (Classic): #C5C0D7
765 Production (Modern): #BBC4E4
765 Production (2005 Orange / GamiP): #FF9900
THE iDOLM@STER CINDERELLA GIRLS
PROJECT CINDERELLA: #8389C3
Cute Pink: #EF8AB5
Cool Blue: #6F8EC8
Passion Yellow: #FABF57
THE iDOLM@STER MILLION LIVE!
Love Live! + Love Live! Sunshine!!
μ's Pink: #E4007F
Aqours Blue: #009FE8
Honoka Kousaka: #E2732D
Eli Ayase: #36B3DD
Kotori Minami: #8C9395
Umi Sonoda: #1660A5
Rin Hoshizora: #F1C51F
Maki Nishikino: #CC3554
Nozomi Toujou: #744791
Hanayo Koizumi: #54AB48
Nico Yazawa: #D54E8D
Chika Takami: #F18D00
Riko Sakurauchi: #FF7777
Kanan Matsuura: #16D5A6
Dia Kurosawa: #FF4242
You Watanabe: #49BBEE
Yoshiko Tsushima: #C3C3C3
Hanamaru Kunikida: #E6CE0B
Mari Ohara: #C450FF
Ruby Kurosawa: #F273C4
Wake Up, Girls!
Maya Red: #E76259
Airi Cyan: #67C5DF
Minami Yellow: #FDE753
Yoshino Blue: #1C62A7
Nanami Purple: #9F65C9
Kaya Green: #64CF76
Miyu Orange: #FF8E44
Wake Up, Girls! Green: #006835
Wake Up, Girls! Blue: #005D8B
BanG Dream!
Poppin' Party Pink: #FF3B72
Afterglow Red: #E53343
Pastel Palettes Green: #23E6A4
Roselia Blue: #5B67FF
Hello Happy World Yellow: #FFA912
Walküre
Walküre Pink: #FF9BD0
Mikumo Guynemer: #7C549F
Kaname Buccaneer: #F9C03C
Makina Nakajima: #EA609F
Reina Prowler: #9CC813
Freyja Wion: #E95364
Dragon Ball Super
Super Saiyan God: #D60363
Super Saiyan Blue: #05BDCD
Mastered Ultra Instinct: #C0C8D8
Pop Team Epic
Pop Team Red: #E6190F
Pop Team Blue: #0046A0
Mario & Luigi: Superstar Saga
Mario: #F80808
Luigi: #18E800
Mario & Luigi: Partners in Time
Mario / Baby Mario: #F00810
Luigi / Baby Luigi: #10F830
Mario & Luigi: Bowser's Inside Story
Mario: #F81800
Luigi: #00B858
Bowser: #F89008
Mario & Luigi: Dream Team
Mario: #FF2211
Luigi: #00DD11
Mario & Luigi: Paper Jam
Mario: #FF0000
Luigi: #00FB16
Paper Mario: #FFBE00
Mario & Luigi: Superstar Saga + Bowser's Minions
Mario: #EE1122
Luigi: #11AA33
Bowser's Minions: #FF0000
Enemy Minions: #0099FF
Yo-kai Watch
Yo-kai Pink: #E08AB8
Yo-kai Green: #66B83C
Yo-kai Blue: #33B6EA
Yo-kai Purple: #938AC1
Sonic Mania
Mania Yellow: #F6CA11
Mania Blue: #385CAE
Mania Red: #E63C2E
Mania Sea Green: #6ACDB1
Mania Orange: #FD8204
Super Mario Kart
P1 Orange: #F86800
P2 Green: #00F800
Panel de Pon / Tetris Attack
P1 Blue: #0050D0
P2 Red: #A00018
Puzzle Bobble / Bust-a-Move (SNES/SFC)
1P Green: #48F868
2P Blue: #48D8F8
Street Fighter II (SNES) + Street Fighter II Turbo: Hyper Fighting (SNES/SFC)
P1 Blue: #00A0F0
P2 Red: #E82800
Super Street Fighter II: The New Challengers (SNES/SFC)
P1 Red: #E01000
P2 Yellow: #D0A000
Mario Party 9
MP9 P1 Blue: #37AED9
MP9 P2 Red: #D64040
MP9 P3 Green: #40B440
MP9 P4 Yellow: #DEC438
Mario Party: Island Tour
P1 Blue: #2626FF
P2 Red: #EC1F1F
P3 Green: #0BCA14
P4 Yellow: #F4C300
Mario Party 10
MP10 P1 Blue: #0071F9
MP10 P2 Red: #EA2F31
MP10 P3 Green: #0EB919
MP10 P4 Yellow: #FCC020
Mario Party: The Top 100
P1 Red: #F10F40
P2 Blue: #0096EB
P3 Green: #16D96E
P4 Yellow: #F7B700
Wii Party
P1 Blue: #1994FF
P2 Red: #FF3131
P3 Green: #21BD21
P4 Orange: #FF9400
Google
Google Red: #EA4335
Google Blue: #4285F4
Google Yellow: #FBBC05
Google Green: #34A853
Google Gray: #9E9E9E
Google+ Red: #DB4437
Google Environment Green: #8AA326
Google Assistant Silver: #959CA5
Microsoft
Microsoft Red: #F25022
Microsoft Blue: #00A4EF
Microsoft Yellow: #FFB900
Microsoft Green: #7FBA00
Microsoft Ignite Red: #D83B01
Microsoft Office Red: #EA3E23
Microsoft Band Purple: #783BD2
NASCAR
NASCAR YELLOW: #FFD659
NASCAR RED: #E4002B
NASCAR BLUE: #007AC2
Super Mario (from Nintendo's Japanese Super Mario website)
Mario Red: #E0120F
Luigi Green: #08A936
Peach Pink: #F096BE
Toad Blue: #17419A
Bowser Gold: #F8BE10
Yoshi Green: #70B921
Daisy Orange: #EE830A
Wario Yellow: #F5DA0F
Waluigi Purple: #5D2E8E
Rosalina Cyan: #1DD4B7
Bowser Jr. Yellow: #F7CE09
Boo Silver: #95A4AE
Donkey Kong Brown: #742607
Diddy Kong Dark Red: #983106
Super Mario Red: #E6280F
Super Mario Blue: #00A0DC
Super Mario Yellow: #FFD200
Super Mario Green: #46AF37
Pokémon
Pokémon Yellow: #FCCF00
Pokémon Blue: #2468B1
NicoNico Douga
NicoNico Switch Green: #1AC3A4
NicoNico Beta Blue: #059BCD
NicoNico Chokaigi Red: #E60021
NicoNico Chokaigi Event Red: #C82762
NicoNico Chokaigi Event Blue: #0B7CAB
NicoNico Chokaigi Event Yellow: #E3D254
NicoNico Chokaigi Event Green: #65BF97