My driver's door had that same problem and the Honda dealer couldn't even fix it for the previous owner. It took me quite some time to finally figure it out.
One of the rubber guide channel pieces inside the door had come out of its proper location, and when the window went up it was folding over one side of the rubber guide, causing the glass to bind up really bad. The only reason I found it (thanks God) is that while working inside the door I dislodged it and it fell inside the door to the bottom. That's when I could see where the glass was rubbing on the wrong area. The piece is in the back side of the door (closest to the latch mechanism), below the window opening.
You're going to have to remove the door panel and the moisture barrier in order to get in there (flashlight, inspection mirror) and see what is going on. It could be a misadjustment issue as well - if the glass is too sloppy between the two guide tracks in the door it can slip out of place.
While you have the door panel off, make sure that your drain holes in the bottom of the door are clear of debris as well. A cannister vacuum hose with a crevice tool works great for this.
After fixing the misaligned rubber part and adjusting the guide tracks, cleaning out the guide channels with compressed air and lubricating them with silicone spray, wowee does the window work nice!
