Cottage can mean any of a variety of generally small informal houses, like this:
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You can make your house look more like a "cottage" by using cottage style gardening, picket fences and the like.

I used to hear bungalow used pretty much the same way, often to refer to vacation homes. Now I almost always hear it used to refer to Craftsman style houses, like this:

I don't think they are entirely separate, as a bungalow can be a cottage. Bungalows originally were 2-story homes, and now most of them are 1- to 1-1/2 story homes. These houses were sort of prefab houses and smaller in size than grandiose homes had some of the same features of the grandiose homes but allowed the owner of much lesser means, at a smaller price, much smaller, to have some of the same amenities as the upper class.

The cottage was meant as a retreat to the upper class but had all the necessities, many of which were 2-story, some were 1-story. Compare to the cotswold cottages. Some of the cottages in the Northeast were belonged to the quite-well-to-do and were retreats and many were second homes along the coast as a retreat for those living inland.

I am sure an architect or someone who has studied architecture or loved it, e.g., New Home Builder, can explain it better. It's kind of like porn, I can see the difference but it's hard to explain. Do a google for "bungalow houses, definition," and "cottage homes, definition" and probably Wikipedia will have better insight.

Here is a very informative article about bungalow houses. It was a very popular building style in my former home of Kansas City...along with mission, victorian, cape cod, tudor, and spanish hacienda. It's a varied town, that's for sure!

I think "cottage" isn't so much a style of architecture as it is a size perception and a style of decorating. Cottage decorating can be done in any style house. You can live in a one room or a two story cottage with a variety of architectural treatments. If your regular house is 3,000 or 5,000 sq ft and you summer in a 2,000 sq ft house, you could still consider the summer house a cottage :)

For me, a cottage is something like the house John Wayne and Maureen O'Hara had in "The Quiet Man". I think small, one bedroom, preferably stone. Some people would call them guest houses :) I could live there, happily, for the rest of my days.

Here is a link that might be useful: Bungalow article

alex I agree the cottage in the Quiet Man was adorable( and all of her blue and white china)