For smaller projects I think ziplock bags are the best way to store a project. And frequent hand washing is a must. The problem with large projects is finding something to keep them in and more importantly transport them ... as I have to do every other weekend. If push comes to shove I have used an unscented, white garbage bag to wrap around my framed piece. With all the spring pollen and sudden rainstorms here cloth just doesnt always cut it....
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My best tip is to keep the thread short, especially if you are stitching on a high fabric count. I cut my thread at 12 inches because by the time Ive used up that much it is starting to look very frayed.