Two weeks in Honduras should give you plenty of time to hit many of the major sights, get you a little bit off the beaten track, and give you a few days to just relax. You'll have considerably more time so you can move at a slower pace -- always a plus in Honduras. You'll be able to take in the beach, the rainforest, and even get your dive certification or have a traditional Caribbean island experience of sunbathing and rum drinks.
Day 1: Arrive in San Pedro Sula and Transfer to Copán
Upon landing, transfer in San Pedro Sula, and head directly to the town of Copán Ruínas. Get settled in and just explore the town in the evening and listen to the adventure tales of other travelers over happy hour to prepare for the weeks ahead.
Days 2 & 3: Explore the Copán Valley
Wake up early your first morning and get to the spectacular Maya ruins of Copán as soon as they open, well before the crowds begin to arrive. Have lunch at the park, and then check out the Museum of Mayan Sculpture and Las Sepulturas. In the afternoon, take a leisurely stroll through the eco-trails of the jungle surrounding the ruins to look for coati, monkeys, blue morpho butterflies, motmots, and dozens of other rainforest creatures. Go back to the hotel, wash off the grime, change into a nice outfit, and head to Hacienda San Lucas for a five-course dinner accompanied by South American wines.
On day 2, head into the nearby mountains to visit one of the Chortí Maya communities, such as La Pintada. Watch as they show you their traditional ways of producing pottery and colorful cornhusk dolls.
In the afternoon, stop by the Museo Regional de Arqueología Maya and browse the handicraft markets for gifts or souvenirs.
Days 4, 5 & 6: Culture and Cloud Forest
On day 4, head to the colonial town of Gracias, once the capital of Central America. Drop off your bags and set out by private tour or your own vehicle to explore the small villages and centuries-old whitewashed churches along La Ruta Lenca. On day 5, set off early to begin your guided ascent through the cloud forest of Montaña de Celaque National Park. Camp at the summit and make your way back down to town the following day with open eyes to spot the elusive resplendent quetzal. Upon your return to town, eat a traditional Lenca meal at Rinconcito Graciano, and then retreat to the municipal hot springs to soothe those aching muscles.
Days 7, 8 & 9: Birds & Brew
On your return north, stop off for a day at Lago de Yojoa, basing yourself at the wonderful D&D Brewery, the country's first microbrewery. The next day, take an early morning bird-watching trip on the lake or head up in the hills at Cerro Azul Meámbar National Park or Santa Bárbara National Park.
Transfer from Lago de Yojoa to La Ceiba in time for a Garífuna lunch at Chef Guity's. Spend your afternoon kayaking at Cacao lagoon or hiking in Pico Bonito National Park.
On your second day in La Ceiba, head out to Cuero y Salado Wildlife Refuge, a massive estuary with almost 200 species of birds and other rare wildlife such as caimans, West Indian manatees, ocelots, monkeys, and sloths. You'll explore the canals and mangrove forest in what is without a doubt one of the most important natural reserves in Honduras by boat from the visitor center at Salado Barra.
Days 10-14: The Bay Islands
Now that you have hiked plenty and spent a good deal of time visiting national parks and major attractions, it's time to kick back and relax in the Caribbean sun and surf. From La Ceiba, catch a ferry or plane for a short trip to Roatán, the most developed of the Bay Islands. Here, you can explore West End Beach and dive on the world's second largest barrier reef. In 3 or 4 days, you can attain a basic PADI dive certification or head to Anthony's Key for an introductory dolphin training course, and still have free afternoons to do leisurely beach activities. If you are looking for a little action, take part in zip-line canopy tours or look for pirate booty in the sea caves on the east end of the island.