Trademarks from video game companies usually fly under the radar or are for projects we will never see. Nintendo changed that notion with its recent "N64" trademark. It is not clear what the trademark could be but it invites speculation.
The easiest conclusion to jump to from the trademark (English translation here) would be that Nintendo is making a Nintendo 64 Classic with the N64's biggest games. It would make sense, given the success of the NES Classic and SNES Classic. Both sold incredibly well and are marked to return on June 29th until the end of the year. The 2.3 million NES Classics sold out within a few hours, showing the rabid demand for this type of machine.
Packing in a couple dozen nostalgia-soaked games into one small device is alluring to fans and would continue the pattern Nintendo has shown. This seems even more likely given how Nintendo has abandoned the Virtual Console going forward, despite attempts from some hackers. Nintendo does not want people to use the Virtual Console if they can get nostalgia money from people in other more lucrative ways.
Their upcoming new online service also promises classic Nintendo titles, which gives players NES games as long as they subscribe. By locking access to their old games behind a monthly paywall or a $60 to $80 Classic console, it paints a picture of a Nintendo that doesn't want people to get their nostalgia for a cheaper price à la carte.
An N64 Classic would fit into that business model. However, while it is incredibly easy to get sucked into a whirlpool of speculation, nothing has been confirmed. Nintendo can throw a curveball and this could mean something completely different. Or it could go the way of other trademarks and could be something we never hear of or see again. If this is an actual thing, Nintendo may talk about whatever this is next month at E3 or sometime down the line.