This won't really affect Sony that much. They're filing another appeal (afaik, this isn't the first go around), and they bawled to the judge, saying that if they couldn't make their consoles with controllers while this was still in court, they'd lose billions of dollars.
So this ruling is "on hold" while Sony appeals it. By the time Sony runs out of appeals, they will have discarded their Dual Shock roots (which they've already said they're doing with the PS3). It won't matter that they will eventually be ordered to stop making Dual Shocks. The only consequence is that their fine will keep increasing.
As-is, Sony has built up $60 billion on their credit line lately. Because of this, it will be $60.09 billion. Sony has bigger problems than just this ruling.
As for why this isn't affecting Nintendo, here's a basic history lesson. Feel free to correct me anywhere I'm off.
Shortly before the N64's launch, word got out that it was going to have "analog". People "in the know" said it couldn't be done. Not yet. Maybe in a few years. It just couldn't be true. But it was true, and it kicked butt.
The PlayStation didn't have analog. Not wanting to be left behind, Sony said "Oh %#$". Threw out their old controller, and tried to one-up Nintendo with their new "Dual Analog" controller (it was only available breifly in Japan).
Then Nintendo was seen frequently talking to Immersion. And was devilishly grinning, pointing at the expansion slot in their controller. Immersion was making "force feedback" devices. They made large joysticks that had complex mechanisms linked to the stick, which could let you do wonderous things, like let you feel what it's like to stir a bucket of paint. They also cost many thousands of dollars. People in the know said "*$@% no. No #&$@ way. I don't care what miracles Nintendo has pulled off, with their '$200 SGI Workstation' and 'analog controls' and all that jazz, there is no freaking way they're putting force feedback into a videogame console. It's just not possible."
Then Nintendo unveiled (and patented) the Rumble Pak. A motor with messed up balance.
The industry started blurting out a mixture of "WTF! That's not REAL force feedback! Ha ha ha! I knew it! I knew I wasn't wrong!" and "That's so simple. Why didn't anyone think of this before."
Immersion apparently said "WTF? It's so simple. And it was right under our noses. We were looking in the wrong direction." Immersion then apparently grabbed all the "old junk" laying around their office and ran to the Patent Office.
Apparently, Nintendo holds the patent on force feedback, by way of an unbalanced motor. Immersion holds the patent on a balanced motor spinning an unbalanced weight. Nintendo was apparently happy to let Immersion have that patent, since they were the ones who unintentionally gave Nintendo the idea for it in the first place, and Immersion began licencing out their brand of rumble technology.
Sony saw Nintendo's Rumble Pak unveiling, and said "Oh %#$. Our controller isn't expandable. We don't have force feedback, or rumble, or whatever you want to call it. We're screwed again. Quick, throw out that Dual Analog before anyone else buys it, and redesign the controller again."
Sony looked at the Rumble Pak and saw that they could seperate the weight from the motor, thus getting around Nintendo's patent. They launched the "Dual Shock" and tried to patent it. The Patent Office said "Bzzzzt! Patent denied! That technology already belongs to Immersion". Sony shrugged, and strolled off, whistling nonchalantly.
When Immersion noticed that Sony's Dual Shock was unpatented, and was using their technology, they started suing Sony.
Microsoft walked blindly into the situation, assuming that it was just "the thing to do" when making a console, but when Immersion called them on it, they apologized and settled out-of-court.