1. Maharaja (also spelled maharajah) comes from the Sanskrit words maha meaning "great" and raja meaning "king". It was and is used primarily for Hindu potentates. The female equivalent to Maharaja is Maharani (or Maharanee), a title used either by the wife of a maharaja or by a woman ruling in her own right.
On the eve of independence in 1947, India (including present day Pakistan) consisted of more than 600 princely kingdoms each with its own raja (if the king were Hindu) or nawab/sultan (if he was Muslim).
The British directly ruled 1/3rd of India, the rest was ruled by the above mentioned princes under the considerable influence of British representatives in court.
The word maharaja may be construed to be simply "king" (as in Jammu and Kashmir), in spite of its literal translation as "great king". This was because only a handful of the kingdoms were truly powerful and wealthy enough for their rulers to be entitled kings; the remaining were minor principalties, towns or groups of villages. The word, however, still means emperor in contemporary Indian usage.
2. In Malaysia, the title of the monarch of the state of Johor from 1873 to 1885. The tile sultan was adopted later and is in current usage.
3. Part of titles of Malay nobility, the most famous of whom was Bendahara Seri Maharaja Tun Mutahir of Malacca (executed 1509) and Datuk Maharaja Lela Pandak Endut of Perak (executed 1876). The palace marshal of the Yang di-Pertuan Agong (king) of modern Malaysia is called Datuk Maharaja Lela Penghulu Istana Negara.