He subsequently lived for a time at Oxford, but in 1857 went to reside at Bushey, Hertfordshire, where he died on 27 Dec. 1858, and was buried on 4 Jan. following in Bushey churchyard.
While at Lampeter he married Mary, only daughter of Thomas Evans of Llanilar, Cardiganshire (who predeceased him on 16 Aug. 1854), and had by her six daughters, five of whom survived him. The eldest, Jane Eliza, in 1861 married Major Walter Colquhoun-Grant of the 2nd dragoon guards, who died the same year in India. She occupied for many years the position of lady principal of Kidderpore House, Calcutta (where she died on 24 Sept. 1895), being succeeded in the principalship by her fourth sister, Margaret, who died unmarried at the same institution on 12 July 1896. Williams's third daughter, Lætitia (d 20 March 1899), married Mr. Robert Cunliffe, president of the Incorporated Law Society for 1890–1; and the youngest, Lucy, married Mr. John Cave Orr of Calcutta.
An oil painting of Williams by Colvin Smith, executed in 1841 on the commission of some old pupils, hangs in the great hall of the academy at Edinburgh. There is also a marble bust of him by Joseph Edwards in the library of Balliol College, a cast of which is at the University College of Wales, Aberystwith.
Besides being one of the greatest classical scholars that Wales has produced, Williams made a special study of the early history of the Celtic races, and particularly of the language and literature of Wales. The more important of his published works are:
- ‘Two Essays on the Geography of Ancient Asia: intended partly to illustrate the Campaigns of Alexander the Great and the Anabasis of Xenophon,’ London, 1829, 8vo.
- ‘The Life and Actions of Alexander the Great’ (being vol. ii. of Murray's ‘Family Library’), London, 1829, 12mo; New York, 18mo; 3rd edit. London, 1860. These two works were written during the author's rectorial interregnum in 1828–9.
- ‘Homerus,’ London, 1842. The essential unity of the Homeric poems was strenuously upheld by the author.
- ‘Claudia and Pudens. An Attempt to show that Claudia [mentioned in 2 Timothy iv. 21] was a British Princess,’ and that Britain was christianised in the first century, Llandovery, 1848, 8vo.
- ‘The Life of Julius Cæsar,’ London, 1854, 8vo.
- ‘Gomer; or a Brief Analysis of the Language and Knowledge of the Ancient Cymry’ (London, 1854, 8vo), followed in the same year by a ‘second part,’ which contained ‘specimens from the works of the oldest Cymric poets in their original form, with translations’ (cf. Skene, Ancient Books of Wales, i. 8–9). In ‘Gomer,’ his most ambitious philological work, Williams dealt with the origin of language, claiming inter alia that Welsh, in its earliest known forms, contained vocables expressive of abstruse philosophical truths, such as the doctrine of the conditioned. His treatment of the subject obtained the warm commendation of Sir William Hamilton.
- ‘Discourses and Essays on the Unity of God's Will … with special reference to God's Dealings with the people of Christianised Britain,’ London, 1857, 8vo.
- ‘Essays on various Subjects, Philological, Philosophical, Ethnological, and Archæological,’ London, 1858.
- ‘Letters on the Inexpediency, Folly, and Sin of a “Barbarian Episcopate” in a Christian Principality,’ London, 1858. He also brought out in 1851 an edition (since twice reprinted) of Theophilus Evans's ‘Drych y Prif Oesoedd’ (Carmarthen, 8vo).
Before the Royal Society of Edinburgh, of which he was a fellow, he read several papers, two of which, dealing with points of Latin philology, were printed in the thirteenth volume of the society's ‘Transactions’ (pp. 63–87 and 494–563). He also contributed essays on the ‘Ancient Phœnicians’ and kindred topics to the ‘Cambrian Journal’ for 1855–7, and articles on more general subjects to the ‘Quarterly Review’ and other magazines.
At his death he left behind him several unfinished works. These included some slight portions of an autobiography (Bye-Gones, 1874, p. 159). His eldest daughter, Mrs. Colquhoun-Grant, subsequently, as his literary executrix, collected further materials for biographical purposes; but these, together with most of Williams's papers and correspondence, were lost off the coast of Spain, near Ferrol, in the wreck of the steamship Europa (17 July 1878), in which Mrs. Colquhoun-Grant was returning to England from India.
