I've been asked about this before, so here's a thread for anybody interested.
I got tired of my sub box taking up too much space, so I took it out. I got used to listening to my music without the sub, but it was still lacking a bit, so I decided to go the route of 6x9's. While I was working with the speakers, I came to realize that you get better bass out of the front doors than the rears. The only problem with this is that the doors tend to rattle more when you upgrade to a bigger/better speaker.
I used Pioneer (TS-a6961 R) 3 way 6x9 speakers for both the doors and the rear speakers. The box comes with a template on the cover so you can cut the proper size hole for the speakers. I cut out the template, then put it over the existing holes for the speakers and put it into a position where the new speaker would not obstruct the window. I then made the cuts with a Dremel tool, ground down the edges, drilled new holes for the screws, and painted over the exposed metal.
Here are some photos of the install. The front dors are the ones with the speakers mounted vertically, the rear doors are the ones with the speakers mounted horizontally.