You can cross road border at Naxalbari in East (nearest metro, Calcutta, approx 350 km away), if you go to see Darjeeling or Sikkim. You can cross at Raxaul in Bihar, near Muzzafarpur. Next crossing is Sunauli, near Gorakhpur in Uttar Pradesh. This is suitable if you desire to go to Nepal from Varanasi or Lucknow. And also another border is near Pithoagarh in Uttaranchal.
These locations are from East to West. And towns named are Indian towns at the border. Pithoragarh is in hilly region of Kumaon.
If you use Sunauli border, visit Pokhra first, same is true in case you wish to cross at Pithoragarh (this will be a very difficult road and is not really desirable).
Source: Thanks to - http://www.travellerspoint.com/forum.cfm?thread=19028