Official border crossings into Honduras [1] are El Poy and El Amatillo [2] from El Salvador; Aguas Calientes, El Florido, and Cuyamelito from Guatemala; and Las Manos, El Espino [3], Guasaule [4], and Leimus (near Puerto Lempira) from Nicaragua. Several unofficial crossings are regularly used along the more remote reaches of the Salvadoran border and across the Río Coco to Nicaragua.
Entering and leaving Honduras by land is generally quick and easy. The best time to arrive is midmorning, well before lunch break, but most border posts are open until 5 p.m. or 6 p.m. You may be asked to pay a US$3 fee when crossing into Honduras by land, and you should be given a receipt if you do. There are no exit fees.
Those leaving Honduras by airplane are required to pay an exit fee of US$34.04.
Links:
[1] http://www.moon.com/destinations/honduras
[2] http://www.moon.com/destinations/honduras/southern-honduras/the-pacific-coast/san-lorenzo-and-the-tegucigalpa-highway/el-amatillo
[3] http://www.moon.com/destinations/honduras/southern-honduras/the-pacific-coast/the-nicaraguan-border/el-espino
[4] http://www.moon.com/destinations/honduras/southern-honduras/the-pacific-coast/the-nicaraguan-border/guasaule