So a few weeks ago I bought Saints Row 2, and they mentioned this company called Ultor.
Last night I played Red Faction 2 for a little bit, which also mentioned a company called Ultor.
Red Faction and Saints Row happen in the same universe.
This shocked me.

They're both Volition games. So maybe they're just a bit lazy when it comes to fictional corporation names?

I read somewhere that Freespace 3 - before it was canceled, was going to have Ultor in it as well. However, I can't find the link, so take what I said with a grain of salt.

a bit?
you'd have to be REALLY lazy.

They could at least have made an anagram of it. Rotul, or something.

I don't see it as lazy really.
Although I found it wierd that I've been reading a series of short stories by HP Lovecraft, recently watched Dagon which is based on a story he wrote (haven't reached the Dagon story yet though), and playing the Witcher which mentions Dagon in terms that obviously reference Lovecraft (and why not?).
Now that's actually quite spooky (especially since the DVD was a random pick by a rental company from my potential list of 60+ DVDs!).
At least they are re-using their own invention, rather than picking up things from other peoples work.

It's probably just put in as an homage to one of their more well known series. I highly doubt the two worlds are in anyway connected.

Also, The Elder ScrollsUltor takes a huge role in both games.
http://en.wikipedia.org/wiki/Ultor_Corporation

Referencing Lovecraft in a pseudo-horror (or outright horror) story is like referencing Tolkein or Norse Mythology in a D&D game.
As far as Ultor: devs like to make nods and in-jokes. I sincerely doubt that the Saints Row Ultor is meant to be the Red Faction Ultor, but it is a fun thing to pick up on.
That being said, the "Dagon" thing is probably more about the Semitic god. Not EVERYTHING is a nod or reference :p. Sort of like how people kept thinking that killing a White Wolf in Drakensang was a jab at The Witcher (Enhanced Edition (Director's Cut)), rather than just killing a big albino wolf.

my link proves it.

Which was the basis for the Lovecraft stories... and therefore a reference. :P
This just reinforces my point that using such references isn't necessarily lazy, and that I can find it very interesting (seeing how Lovecraft is an influence on so many others, it is always interesting to see what influenced him!).

No, your Wikipedia page (with no references, I should probably go pop up the appropriate template) just shows that Ultor was in all the games. Until Volition themselves admit it is intended to be the same company (either way), it is still fan speculation.
And it is not like authors don't reuse names. Look at John Steakley, he has used the exact same characters in all of his stories (which range from vampire killing bounty hunters to Armor). Somehow, I don't think Felix is a time travelling dimension-hopper. :p
Then by your definition, anyone who has an Elf in the story (even Warhammer 40k, with the Eldar) is referencing Tolkein :p. Well, okay, they probably are, but Tolkein didn't start it.

We're all time travelers.

In both games Ultor has the same name and logo, very similar feel-good mottoes ("revolutionising your future" and the like) and the same motives (ostensibly honest humanitarians that are actually corrupt and organise the murder or sabotage of rival companies or threatening individuals). None of this is just by chance.