The thing that I don't have in my home office (that I really need to address one of these day) is proper lighting.
More desk space would also be nice, which is kind of a laugh if you see just how much desktop real estate I actually have. The problem is, however, that I've got non-office related stuff that needs a place and sadly, my desk is the only suitable location.
More room for files would be helpful. More shelving would also be great.
The one issue I've run into a few times is that because this isn't strictly an office, the decor isn't really officey. While I personally don't care the vast majority of the time, I have found a couple of times when I've been forced to be involved in video/Skype calls, I've had to relocate to to a different room with a much more neutral background.
As people have said, make sure you've got plenty of outlets and that they're located in places that are actually useful and accessible.
While bazza mentioned not ruining the carpeting, you also have to worry about not ruining the hardwood flooring (or other type of non-carpeted flooring like tile). Sadly, I didn't take this lesson to heart soon enough, and the hardwood under my chair definitely shows more wear than the rest of the floor. I've got a run now, but the damage is done.