I'm thinking specifically of the Azores and Madeira Isles, because they strike close to home (am Portuguese), and how they were discovered (or re-discovered) by men in small ships. Looking at their size in the middle of the Atlantic Ocean makes me wonder what were the processes used by the captain to decide where to go, out of the blue sea. It boggles my mind even further to think of the tiny isles in the much larger Pacific Ocean.
I can think of birds and cloud formation above the isles, as well as possible breeze due to the presence of land, but I wonder if there were other methods used.
I'm not sure that they were necessarily looking for them, but I can't find any thing comprehensive on that. The Azores are along favorable trade routes, so one of the quickest ways to get back to Portugal from West Africa is to sail north to the Azores and then sail due east back to Portugal.
So, even if they weren't looking for them, they probably would have gotten discovered pretty early on anyways.
http://en.wikipedia.org/wiki/History_of_Portugal_(1415%E2%80%931578)#Sailing_techniques