If seems that every company has a flagship yoyo. The throw that represents the company as a whole.
Let’s see if we can name them all.
Clyw- chief
And I would argue that yyj would be the dark magic.
Go!
General Yo-- 5 star, maybe Majesty when more runs are made, but the 5 star is what Genyo is know for.
I can also say that Adegle is the Psg( plastic sand glass)
YYF - 888 or the genesis
Turning point - Positron
Onedrop - code 2? Not sure on this…
One drop- Cascade/Code 2
This is arguably the Peak. Chief maybe in the “modern” era, but really it’s the Peak.
To me, flagship yoyos are ones that are still being produced, which causes some to be ommitted. Most notably, the CLYW Peak and OD Project.
YYF - 888, Genesis, Supernova
YYJ - Dark Magic
CLYW - Chief
OD - Code 2
C3 - Capless
SPYY - Addiction
It’s hard to say which one of General Yo’s models is their flagship yoyos, as they are one of the only companies that only produces one throw at a time, and once they are done, no more will be produced. For some it is the Torrent, their first throw. The legendary yoyo that DEFINED absolute smoothness and set the bar for all companies. For some it is the 5 Star, a similar yoyo to the Torrent. It just has that General Yo feel. For MOST people it is the Hatrick. For whatever reason, it is the Hatrick. This was probably one of the most hyped yoyos ever, for a very long time. It’s a legendary yoyo as well, If I had to give you an answer right now, I would say the Hatrick. It’s pretty much the yoyo that gave General Yo their popularity and when it was released their presence in the yoyo community seemed to skyrocket. To the newer throwers of General Yo, they might say the newest throw is their flagship, which in this case is the Majesty. But before the Majesty, was the KLR and that to many was the flagship yoyo. It will always be topped with General Yo, which is why I would say the one of the first 3 releases (Torrent, 5 Star, Hatrick) would be one of their flagship throws. The best one certainly is the Majesty, but that’s a whole different topic. 
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Duncan is a tough one. The imperial butterfly for the non throwers, the fhz for the throwers would be my guess
Yyf- 888
CLYW- Peak
Od-code 2
Tp-Postitron
YoYoRecreation-Sleipnir, or Stardusts
Duncan- imperial or butterfly
Spin dynamics- smooth move
Spyy- Punchline ( ??? )
Yyf- 888
YYF - 888
C3 - capless
Spyy - addiction
werrd - hour?
Duncan - imperial/butterfly
CLYW - I’d say peak
One drop - Code 2
Adegle - PSG
Toxic strings - hazmat (obviously)
G squared- nessie
General-yo - KLR (IMO)
sOMETHING - Anglam
Tom Kuhn - No Jive
Aoda - free king
All I can think of at the moment
YYF - 888
C3 - Berserker
Spyy - Addiction
Werrd - Irony JP
Duncan - FHZ
CLYW - Chief
One Drop - Code 2
Adegle - PSG
G squared- Albatross
General Yo - KLR
sOMETHING - Anglam
YYJ - Dark Magic 2
Yoyo Recreation - Sleipnir
Turning Point - Positron
Yomega - Raider
Yoyo Joker - Double Joker
Yuki
A flagship yoyo doesn’t have to be the most popular one, which is why I’m not sure about C3 and the Capless. I think a company’s “flagship” is the one they think best represents them as a brand. It’s not usually “the” most expensive product, but is also not the budget option.
I HAVE a Capless and it’s a wonderful throw, but I would think the company themselves would see any number of other throws as more flagshippy than the Capless. Trident, Dark Sonic, Yeah 3, Berserker… I dunno which, honestly! But probably not Capless.
For the same reason, I doubt Adegle thinks of the PSG as their flagship.
Dif-e-Yo: Rev. 1 Overhaul
TenYoYo: Drop Bear
Chico: ??
this seems familar.
C3 considers the Berserker tone it’s flagship
Not the capless