If You Have 3 Days: After arrival in San Pedro Sula, head southwest to the town of Copán Ruinas and get settled into your hotel. Take one day to explore the Mayan ruins. You can walk there from town or take one of Copán's fun tuk-tuk (three-wheeled) taxis. If you're like most visitors, you'll pack your second, and only remaining, day here with all the other activities for which the area is known: a bird park, a butterfly garden, zip lining, horseback riding, shopping... the list is endless. Treat yourself to a third day, and you won't have to cross any items off your to-do list.
If You Have 3 to 5 Days: Begin in San Pedro Sula and head southeast to Comayagua. (You can begin in Tegucigalpa, too, in which case head northwest.) A day gives you ample time to take in Comayagua's four main colonial churches and the archaeology museum. If the museum of religious art has reopened by the time you read this—it was badly damaged in a 2009 fire, and still closed at this writing—that's a must-see, too. After spending the night in Comayagua, head north to Lago de Yoja along CA-5, the highway connecting San Pedro and Tegucigalpa. Bird-watching and hiking easily fill several days here. You can probably just show up if you come during the week, but weekends get crowded here at the lake so make reservations. Top off your lake visit with one of D&D Brewery's microbrews.
If You Have 5 Days: A visit to Copán from San Pedro Sula occupies three days, but tack on an excursion to Santa Rosa de Copán and Gracias, two of Honduras's premier colonial cities. Unfortunately, no road connects Copán Ruinas to Santa Rosa, meaning you must backtrack to the crossroads town of La Entrada. That does add a couple of extra hours. However, once there, you can base yourself in either Gracias or Santa Rosa—both have good lodgings to choose from—and visit the other as a day trip.