I'm a fan of reusing bottles. I'm using a 1 quart/1 liter Gatorade bottle instead of a Nalgene for holding/purifying my water. I'm terrible at remembering to clean stuff after coming back from a camping trip, and I'd rather a Gatorade bottle go slimy than an expensive "reusable" bottle.
99% of the time, this isn't an issue. My Steripen fits inside the bottle barely, and so I can still use it. As long as the water comes up to the very top, the contacts can be submerged, and the Steripen will operate.
The problem comes when the water isn't deep enough to fill the water up to the top of the bottle. Quick and easy solution is to create a water scooper. This can be made from the bottom of a water or soft drink bottle.
The other problem is that when using a bandanna to filter out guck, you either have to pour the water very slowly or expect to lose most of it off the sides. If you use a funnel, however, the water can take as long as it needs to filter through the bandanna. And fortunately, the top of the same bottle as above can be used as the funnel (see diagram). You simply place the bandanna over the Gatorade bottle, insert the funnel, and then pour water from the scooper into the funnel. It takes a few minutes to fill a 1-liter bottle with this method, but it works. And this would only be needed if the water is cloudy or has floaties.
The final question is, how much space does this take up? Well, if you have external water bottle pockets, I put the funnel at the bottom of the pocket, then my Steripen, and then the scooper upside-down on top of both. It keeps the Steripen from falling out of the pocket as well, so it works great for my usage.
Price: Between one and two dollars for the bottle, plus a bandana
Build time: 5 minutes
Availability of materials: Smart Water is sold everywhere around here; a soft drink bottle would probably work just as well.
Durability: Should last for a while, and it can be rebuilt at any time
Functionality: Works efficiently, if a little slowly
Portability: Fits with the Steripen into a water bottle pocket