Babington wrote on a variety of subjects. His early familiarity with country life gave him a taste for natural history, especially botany and ornithology. He was also an authority on conchology. He was the author of the appendices on botany (in part) and ornithology in Potter's History and Antiquities of Charnwood Forest (1842); Macaulay's Character of the Clergy (1849), a defence of the clergy of the 17th Century, which received the approval of Gladstone. He also brought out the editio princeps of the speeches of Hypereides Against Demosthenes (1850), On Behalf of Lycophron and Euxenippus.(i&Ss), and his Funeral Oration (1858). It was by his edition of these speeches from the papyri discovered at Thebes (Egypt) in 1847 and 1856 that Babington's fame as a Greek scholar was made. In 1855 he published an edition of Benefizio della Morte di Cristo, a remarkable book of the Reformation period, attributed to Paleario, of which nearly all the copies had been destroyed by the Inquisition. Babington's edition was a facsimile of the editio princeps published at Venice in 1543, with an Introduction and French and English versions. He also edited the first two volumes of Higden's Polychronicon (1858) and Bishop Pecock's Represser of Overmuch Blaming of the Clergy (1860); Introductory Lecture on Archaeology (1865); Roman Antiquities found at Rougham (1872); Catalogue of Birds of Suffolk (1884-1886); Flora of Suffolk (with W. M. Hind, 1889), etc. He catalogued the classical manuscripts in the University Library and the Greek and English coins in the Fitzwilliam Museum.