Underwater Vision, Utila

http://www.utilascubadiving.com.

Utila has plenty of different dive shops, our choice was Underwater Vision one of the biggest dive shops on the island.
The shop has a bar/restaurant (always look for the daily special), hammocks and a volleyball field. All the staff are kind of a family, so be open and they will welcome you.
Underwater Vision offer all courses from Open Water until Instructor and higher. Every course includes a few days free accommodations otherwise you can stay in the dorm for 5 bucks a night. All prices and details about the courses and more can be found online.

Buzos de Mexico, Isla Mujeres

http://www.buzosdemexico.com/

We found this nice place only by accidents while looking around for another dive shop. The owner, Misael, is half swiss so he talked us into to take a look around the shop. He showed us his new equipment and the big boat he has to go diving. His mother, Pia, rents out rooms just above and behind the dive shop, with a little discount for the diving.
Thats how we ended up with a room just above the dive shop and by chance Patricks instructor, Nathan, was swiss as well. We liked it so much we stayed much longer than planned. Diving with Nathan was really relaxing, we did a wreck, drift ;) and night dive besides the usual reef dives.
The boat leaves form the pier at the restaurant/museum of Capitan Dulce where they are building a new dive center/shop/storage. At the moment there was only the grass roof, but looks to become nice!

Little advice: If you plan on going to snorkel with the whale shark, check if they are going out on their own big boat. If not just shop around for the cheapest tour to go, as all are more or less the same.