These are all I could Think of off the bat:
Duncan
YoYoFactory
YoYoJam
Spyy
CLYW
ILYY
One Drop
General Yo
Big Brother
44re:creation
Spintastics
Tom Kuhn
Bist
Barco
3Yo!3
Werrd
Who can Name the Most YoYo companys with out looking
YoYoFactory
YoYoJam
Duncan
Hugo Z Hor
Auldey
Takuto.Design
B!st
SPYY
CLYW
General Yo
YoYo Recreation
One Drop
Big Brother YoYos
Tom Kuhn
Werrd
3Yo3
I love yoyo
String Theory Yoyos
Yomega
Bandai (Yes Really)
AODA
Alchemy
HiCOO
Born Crucial
Madhouse
Oxygene
Anti-Yo
You guys are all forgetting HSpin? 
Wow. I feel ashamed…
Don’t forget Rec-Rev…
IKYO!
yyf
yyj
zeekio (yoyosam’s brand)
BBYY
1drop
ICKYO
rec rev
h spin
crucial
alchemy
hugo (not sure what the name is but they made the hugo z hor)
tom kuhn
duncan
bandai
clyw
spyy
hicco (probably spelled wrong)
3yo3
madhouse
general yo
ilyy
now its getting hard to think of more lol
jazz yo
death by yoyo
vs newton yoyo concepts
anti yo
kyo
x-yo (i think thats the name)
yomega
aoda (doesnt really count since they rip off everything)
turning point
chico yoyo company
oxy
b!st
AnY yo (or yoyo i cant recall)
and thats all i can think of off the top of my head
heres my list…
44re:creation
Aerobie
Alchemy
3yoh3-----LOL (3oh3)
Turning Point
AnY Yo
Anti-yo
B.I.O.
BBYY
Japan Technology
Tom Kuhn
Chico YoYo -----I think?
BC
B!5T
Bandai Yoyos
Black Mamba Snake
Blazing Teens ----AUDELEY
Born Crucial
Buzz-on
Dif-e-yo’
Duncan
Caribou Lodge YoYo Works
Custom
Saturn
Shinwoo
General Yo
HICOO
RooYo
Hspin
Henrys
Proyo
ILYY
Kyo
Russel Wooden Yoyos
Spintastics
SuperYo
Team Losi
Throw Down
YoYoFactory
YoYoJam
Yomega
Jazz-yo
Broken YoYos
Cold Metal
OneDrop
SPYY
Madhouse
Oxygene
String Theory
Brent (ibanezcollector) Painted YoYos
Werrd
Roll-out
K2J
------All i can remember-------
~gorrilla_yo 
Interesting how most of them are in alphabetical order, huh?
i know huh except for the last ones
I feel suspicion in the air!
duhn duhn duuuuuuuuuuuuuuuuhn!
Really Tyler? lol its IKYO. Look at my awesome JM sig!
No joke…i just thought it off the top of my head and wrote it down…made a list that took me like 20 minutes to make then i posted…there not in alpha order…it may look like it but it’s not…
Whoever said it was in alphy order (I’m not going back to look) should go back and look! lol
Yeah, check this out. I only kind of like I don’t know said it correctly earlier…
Did Everyone Forget Zan Navi?
Yea. Shinwoo Zanavi rox
Can i join?
Let see . . . .
YYF
YYJ
44re / yoyorecreation
Hicco
Takuto design
Auldey (not much to say. Nice virus and L3 though. And i still lookin for inca)
Aoda (with many rip off. But i realy like the royal star)
3yo3
Rosyo (indonesia by oke rosgana)
Adegle (taiwan)
C3 (hongkong)
Dif-e-yo
K2J (china)
Jazz yo (also chinese)
Cowa (another chinise)
1drop
Rec Rev
Kyo
X-yo
Yoyojoca
Tom Kuhn
Chico yoyo
Hot yo
Mad house
General yo
Hspin
Japan technology
T3K (belgium)
B!ST
Buzy On
Throw Down
Alchemy
Big Brother Yoyo
Death By Yoyo
Crucial
CLYW
Cold Metal
Duncan
ILYY
Oxygene
Rollout
SPYY
Werrd
Yomega
Anti Yo
AnY
Turning Point
Shinwoo
Japan techology
Radiyoactive
I cant think any again
This thing make me busy for almost 20 minute
(Psst. Zan Navi isn’t a company. Shinwoo is. :P)
Kristiawan said Japan technology twice and accidently put Buzy On. You guys know a lot though.