From Bali in the west to Timor in the east, the classic island-hopping backpacker trail across Nusa Tenggara runs something like this:
Ferry from Padangbai, Bali to Lembar, Lombok
Overland across Lombok via Senggigi
Ferry from Labuhan Lombok to Poto Tano, Sumbawa
Overland across Sumbawa via Sumbawa Besar and Bima
Ferry from Sape to Labuanbajo, Flores
Overland across Flores via Maumere to Ende
Ferry from Ende to Kupang, West Timor
Overland across Timor to Dili, East Timor
Popular detours include visiting the 3 Gili Islands lying a few km of the western coast of Lombok and Komodo north of Flores. Less popular options include going via Sumba instead of Flores.
A night time ferry also runs, sometimes, from Waingapu, Sumba to Ende, Flores, taking about 11 hours.