If you are trying to save large amounts you may have been recommended to stay on the islands and book day trips. This is definitely an option and you can go on some great trips. However I think that having decided to do the Galapagos you should experience everything it has to offer. Here are some useful things to consider when making this decision.
With the exception of Isabella and Saint Cristobel day trips set off at 730am and return the same day. This immediately limits the distance that you can travel around the islands. As a result there are many islands that you are not able to visit on day trips. For me, these are the islands that offer the most. Espanola, Fernandina, Genovesa and Floreanna are the 4 most highly rated islands according to me and everyone that I spoke to around South America. Of these Floreanna is the only one that you can access on a day trip.
Another thing to consider is that many of the islands are wide spread and involve long boat crossings. The cruise schedules are designed so that you make most of long notoriously bad crossings over night when you are sleeping. You are also on board a larger vessel and therefore the motion is less exaggerated. Finally, if you are on a day boat, all passengers are confined to a small area so if someone is very annoying or violently sick, you are stuck next to them for the duration of your crossing. So it may be a good idea to take headphones and a few spare sea sickness tablets.
There are a few hostels around, however for what they offer, they are not very economic. When you consider for a day trip you are paying $110-$150 a day plus evening meals and accommodation, you don’t save much compared to a cruise.
Having completed a cruise followed by a day trip I have to say I found the latter experience comparatively underwhelming. However the experience is still incredible.