IMO:

Epic Games -> Mark Rein made it clear he doesn't like Nintendo platforms.

Bethesda -> Todd Howard told in an interview he doesn't like Nintendo.

EA -> Half-assed versions and lame support from it. Historically they were never close either.

Take-Two -> They barely support Nintendo systems. Reasons are unknown.

Rockstar -> Mostly because of DMA Design. I don't blame them, Nintendo blew it hard with Body Harvest.

Infinity Ward -> They told COD4 couldn't be done on Wii and Treyarch prove they wrong.

Ready at Dawn -> Bashed Wii in a interview and never worked with Nintendo systems ever since.

Who else?

Naughty Dog -> Won't port Uncharted 2 to DS

For the most part, most companies that don't support Nintendo heavily would fall into one of two categories; those that have made business decisions that put them at odds with Nintendo's strategy, and those that have limited resources and are directing them in the way they believe will maximize their results.

While Mark Reign is a douchebag, Epic on the whole is a company that I would say is just at odds with Nintendo's business strategy ... Nintendo wants to keep development easy and inexpensive enough that small developers and creative ideas continue to thrive; Epic makes money as game budgets skyrocket and developers are willing to spend more money on their development tools.

Valve - i guess

lol

Take-Two -> They barely support Nintendo systems. Reasons are unknown.

Rockstar -> Mostly because of DMA Design. I don't blame them, Nintendo blew it hard with Body Harvest.

why are these two separate? they are the same company.

Not entirely. Much like how Nintendo gets poor support from, say, EA as a whole or DICE (wholly-owned subsidiary) in particular, which is also true, but both may have different reasons for not doing so.

I would say the most prominently anti-Nintendo developers seem to be a certain branch of PC-focused developers. The most anti-Nintendo ire seems to come from groups like Epic, iD, Bethesda, BioWare, and DICE. Companies who honestly have nothing to do with Nintendo, like Valve or Blizzard seem to be on decent enough terms (that is to say, they never say anything about them,) but these PC developers that have a controlling interest in multiplatting their games to consoles seem to have varying degrees of distaste for Nintendo and what they do, which could stem from the fact that Nintendo's trying to subvert the model of consoles being wannabe PCs

Rockstar is an honest-to-goodness case of prior bad blood that is more Nintendo's fault then not, the rest is just sour grapes

Ready at Dawn has made 4 games. One was a Wii port of Okami. I really don't think they matter.

Take Two made those Carnival Games didnt they??? Didnt they sell like millions??? Id call that support, dont know WTH happened to the last game

Matter? In terms of what?

They've sold a few million copies of their games and have a lot of talent in their studio- former Blizzard and Naughty dog devs included if I'm not mistaken. In a few years they could well expand beyond the handheld space.