Looking at the Cool moisture humidifiers i own they are pretty simple machines. Water sits in a shallow tray, is wicked up into the filter where a fan draws air threw the filter picking up moisture and blowing it out the front. So i figured a simple water tight box, a 80mm PC fan, 20 oz bottle of water and humidifier filter would make a decent setup.
For the container i had an old baby wipes container. Since the top is such an odd shape i removed most of it and fitted a piece of scrap aluminum i had around the house. I also had an 80mm fan but needed to supply power to it. Fortunately when old electronics die i hold onto the remains. I happen to have a AC/DC power adapter from a battery charger. It puts out 16VDC at 1A but it not too much for the fan. I also had a switch handy as well as a power plug that fit the adapter.
The first thing to do was cut the hole for the bottle. So i cut a hole just shy of 3" in diameter which was perfect to just squeeze the bottle through the hole and have it bottom out in the container. So the bottle needed to be modified to allow the water to fill the bottom of the container by about 1/2". Thus giving enough depth for the filter to soak it up.
Once i was sure that a couple of bottles full of water dumping into the container wasn't going to touch the electronics i cut the fan hole and switch hole. The removal of the top section left a big gap between the aluminum plate and the front lip of the lid. This was the perfect place to put the power plug. The filter was placed on the bottle side of the container since the bottle would help hold it against the side. So i didn't need to create any kind of brackets.
It took a good 6 hours to complete from start to finish and thats with feeding kids dinner and putting them to bed. Its not pretty but it works. I think a little more attention to detail with the hot glue and a good paint job and it would look pretty good. Overall i'm happy with it. Especially since it didn't cost me a penny to build.
See the full instructable for this here: http://www.instructables.com/id/Desktop-Humidifier-1/