Of all the three towns, Puerto Baquerizo Moreno is the one with the highest percentage of bland, square rooms for about $25 per night. There are a couple of cheaper options, however, as well as some nicer places for those with a little more to spend.
Many of the hotels in San Cristobal are clustered along the waterfront, including, oddly enough, almost all of the high end AND extreme budget options. Get away from the water and all of the hotels start looking the same.
It seems like feast or famine for the Puerto Baquerizo Moreno. The hotels are usually mostly empty, as visitors tend to go to the centrally-located Puerto Ayora or the more hip Isabela. They can fill up fast, however, if there is a conference of some sort going on â€“ remember, Puerto Baquerizo Moreno is the capital of Galapagos. It also may fill up during the annual Galapagos marathon. In other words, book early, even though you may find when you get there that the town is nearly devoid of tourists.