Full list of official camping sites used: List
We did a lot of bush camping once we got to Peru but this list includes only "official" camping sites. Sorry there are no way-points but we weren't traveling with a GPS. We managed to find all of the campgrounds with a combination of signage and asking for directions.
A few select hotels, that we stayed in, in popular areas:
Honduras
La Ceiba – Hotel Posada del Caribe, http://www.hotelposadadelcaribe.com/
Near the mall. Parking garage with secure parking. They were happy to let us leave our bikes for a few days while we went to Roatan. Also, and most importantly, they had a storage room so we didn't have to take all our things to Roatan with us. It was like a $5 cab ride to the ferry.
Roatan [West End] – Posada Arco Iris, http://www.roatanposada.com/
Good location. Has it's own small private beach with lounge chairs and kayaks. Rooms were pretty big with a small deck area that included a table and hammock. Staff was very friendly.
Nicaragua
Granada – Hotel Oasis, http://www.nicaraguahostel.com/
Parking inside hotel on main floor. Nice common areas, internet, small swimming pool.
Panama
Panama City – Residencial Alameda,
Locked parking lot. Large rooms if you are in either 01 or 02 on the floor. Wireless router on each floor. Free porn channel.
Colombia
Cartagena – Marlin Hotel, http://website.hotelmarlincartagena.com/
Across the street from Casa Blanca hostel. Biker friendly parking [read: triangle wedge to turn stairs into a steep ramp to park bikes on main floor]. Fast internet, and a very basic breakfast included. Rooms are very small.
Medellin – Hostel Medellin, http://www.hostalmedellin.com/inicio_in.html
Very biker friendly hostel. If you need any mechanical work done the owner has a few contacts and will help. Parking, internet, hot water.
Ecuador
Quito – Travelers Inn, http://www.travellersecuador.com/Eng/index.html
Secure parking, internet, hot water. REALLY good breakfast included.
Guayaquil – Hostal Suite Madrid, http://www.hostalsuitesmadrid.com/
Secure parking, internet, hot water.
Peru
Huaraz – Hotel Las Tejas, http://www.hotellastejas.com/
Near the main plaza. Parking garage attached to Hotel. Laundry up the street. Wifi + hot water.
Cusco – Hostal Marani, Camern Alto 194 www.hostalmarani.com
Large courtyard to park bikes. Laundry in hotel and across the street. Decent internet and large rooms. Very HOT water. REALLY good breakfast included.