It is honestly surprising that until Nori arrived at Hidamari-sou, there was no Internet connection there. I suppose I'm just too used to living my life online.
We've all seen the standard generic lawyer-friendly versions of brands we all know about, but which come with so much trademark baggage that shows cannot even mention them without jumping through a lot of hoops; even something as innocuous as affixing a ™ sign becomes onerous when it comes to exhibiting it in an anime; I think only studios like SHAFT, which make a name for being ARTSY and all that, can do anything along those lines.
More likely, there will be all sorts of regulations and guidelines on displaying the brand: it cannot be portrayed negatively. It cannot be used in a way other than it is normally intended for. The entire brand logo must be displayed. All this is perfectly understandable, since the brand represents the company's name, both literally and figuratively. (Compare regulations on displaying country flags.)
There have been plenty of other writings, some of them even academic, on the significance and implications of all of this. I am not… well, technically I can talk about this with some degree of accuracy, but this is an anime blog, and I post here to get away from work.
But I do find it interesting that we can recognize all these alterations to the brands we know, because they are the brands we know. We know which fast food chain "WcDonald's" is, or "Zony" mp3 players, or "Packy" biscuit snacks. On that note, Pocky represents an intriguing case: outside of Asia, people seem to know it in conjuction with anime and Japanophilia, but it has been so prevalent, even in lawyer-friendly form, that it is recognizable, even cliche.
Not much can be done for an Apple logo, although attempts have been made by keeping the general shape and colouration of an iBook or iMac or iWhatever, which is pretty distinctive, and substituting other fruits. For Microsoft Windows, apparently four coloured boxes is sufficient.
I can only imagine how anime will deal with Tux.