The rules surrounding overflight of Central America change on a relatively regular basis, but as of January 2016, this is the current status.
Let's start with a CENAMER Notification. What is it, and why do I need one?
CENAMER is a combination of CENtral AMERican countries that work together as one for ATC Service. The controlling Authority is COCESNA. The actual controllers are in Tegucigalpa, Honduras, but control the airspace of Belize, Costa Rica, El Salvador, Guatemala, Honduras and Nicaragua.
For flights intending to operate within that joint Flight Information Region (FIR), COCESNA require notification. Every FIR worldwide requires the same thing, but because of the grouping of countries, the process is a little different for COCESNA. A preformatted AFTN message must be sent containing the flight details and planned schedule, to both the AIS office, and to the various billing departments. The latter is most important, because it give them the opportunity to warn in advance if airspace entry will be denied because of unpaid Navigation Fees. The CENAMER Notification confirmation is normally in the format MPTOXXXX192330, being the originating AFTN address and a datetime stamp.
A CENAMER Notification is required for every flight entering the Central American COCESNA FIR
OK, so that's the Notification. It's important to note that this isn't an Overflight Permit. Each country that makes up the FIR has it's own rules - most require a Permit. Remembering that the CENAMER Notification is primarily related to ATC Service (and paying for it), the Overflight Permit is there so that the Authority can regulate traffic overflying from a Security, Safety, and Regulatory oversight perspective.
Country by country, the Overflight Permit rules are as follows:
Costa Rica: No overflight permit is required; an FPL should be filed 24 hours in advance. Non-commercial flights do not require a landing permit either.
Nicaragua: Requires an overflight permit. The authority levies a permit charge of approximately $127 including bank fees, which must be paid direct to INAC prior to overflight. A landing permit is also required if stopping in the country.
El Salvador: Does not require an overflight permit, or a landing permit.
Honduras: Requires an overflight permit and a landing permit.
Guatemala: Requires an overflight permit and a landing permit.
Belize: Requires an overflight permit and a landing permit.
For all those countries above requiring a permit, the normal Aircraft Documents (ie. Registration, Airworthiness, Insurance, Licenses and Medicals) need to be submitted to the CAA.