Capcom: has released few home console games in general in the last couple of years, and Wii U got about half of them anyway. Mega Man in Smash and terrific 3DS support gives them a positive rep among Nintendo fans acting as a buffer against the hate. That they continue to actively support the growth of the Virtual Console on both Wii U and 3DS is another point in their favor.
Sega/Atlus: Nintendo consoles get many exclusives from these guys. The Persona series is coming to a Nintendo console for the first time later this year. Tremendous support overall even though some games (mainly exclusives) don't come to Nintendo platforms. Bonus points for Colonial Marines not releasing on Wii U. Oh yeah, and they put more effort into their 3D Classics than Nintendo themselves.
Konami: they have not strongly supported Nintendo consoles for a long time. Additionally, it seems Metal Gear Solid is the only thing they can do right any more, so most of their games are not a big loss. Note that Western publishers who also have little history of supporting Nintendo consoles, such as Bethesda, are ignored by Nintendo fans in much the same way.
Bandai-Namco: as with Capcom, I am hard pressed to name major home console titles released by these guys in the past year and the immediate future. The Wii U did get a Tekken game at launch and their cooperation in Smash Bros development gives them some good publicity.
Square Enix: similar to Konami, though Square has a longer history of supporting Nintendo platforms. Of all Japanese publishers, I think SE is the one that gets the most flak from Nintendo fans, rivaling or exceeding the amount of ire directed towards Western publishers. Examples of this include frustration over Kingdom Hearts 1.5 and 2.5 being Sony exclusives and Kingdom Hearts 3 releasing on Xbox, while the Wii U gets nothing despite several installments in the series being Nintendo exclusives, as recently as 2012 on 3DS. There is also frustration over Final Fantasy XV not coming to Wii U: from VII through XII, most gamers took it for granted that main series Final Fantasy titles were Sony exclusives. When the XIII games started coming out on 360, Nintendo fans knew the Wii couldn't handle that game, and didn't care much anyway because the XIII games weren't as popular as previous entries. Now that Nintendo has a powerful console many Nintendo fans see as comparable to the latest generation, some had hopes that major titles like FFXV would be available on all three consoles. The debate about whether XV and KH3 could run on Wii U is well documented and I won't get into that. But suffice to say Square Enix has not gotten a free pass from the general Nintendo fandom.