This is only partial list. There is no claim that only these are great ulema. Many more are there. So list is half and incomplete.This is Student-teacher wise,
I divide the student-teacher relationships into generations. It's easier to connect the names that way:
First Generation:
Hazrat Moulana Qasim Nanotwi (rahmatullahialay)
Hazrat Moulana Mufti Rashid Ahmad Gangohi (R.A
Hazrat Moulana Ya'qub Nanotwi (rahmatullahialay)
Hazrat Moulana Rafi'udeen Deobandi Usmani (RA)
Hazrat Moulana Sa'adat Ali Saharanpoori (R.A)
Hazrat Moulana Mazhar Nanotwi (rahmatullahialay)
Hazrat Moulana Zulfiqar Ali (rahmatullahialay)
Hazrat Moulana Fazlul Rahman (rahmatullahialay)
Second Generation
Hazrat Shaikhul Hind, Moulana Mufti Mahmoodul Hassan Gangohi (rahmatullahialay)
Hazrat Mufti Azam, Moulana Mufti Azizur Rahman Usmani (rahmatullahialay)
Hazrat Moulana Khalil Ahmad Saharanpuri (rahmatullahialay)
Hazrat Moulana Ahmad Ali Muhaddith Saharanpoori (Rahmatullahialay)
Third Generation
Hazrat Hekeemul Ummat, Moulana Ashraf Ali Thanvi (R.A)
Hazrat Shaikhul Islam, Moulana Hussain Ahmad Madani (rahmatullahialay)
Hazrat Imam ul Asr, Allamah Anwar Shah Sahib Kashmiri (rahmatullahialay)
Hazrat Moulana Habeebur Rahman Usmani (rahmatullahialay)
Hazrat Moulana Shabbir Ahmad Usmani (rahmatullahialay)
Hazrat Mufti Azam, Moulana Mufti Kifayatullah Dehlwi (rahmatullahialay)
Hazrat Moulana Yahya Khandelwi (rahmatullahialay)
Hazrat Moulana I'izaz Ali (rahmatullahialay)
Fourth Generation
Hazrat Mufti Azam, Moulana Mufti Muhammad Shafi Usmani (rahmatullahialay)
Hazrat Shaikhul Hadith, Moulana Muhammad Zakariyah Khandelwi (rahmatullahialay)
Hazrat Moulana Idris Khandelwi (rahmatullahialay)
Hazrat Moulana Qari Muhammad Tayyib (rahmatullahialay)
Hazrat Moulana Muhaddith Yusuf Binnori (rahmatullahialay)
Hazrat Moulana Muhaddith Zafar Ahmad Usmani (rahmatullahialay)
Hazrat Moulana Ahmad Ali Lahori (rahmatullahialay)
Hazrat Mufti Azam, Moulana Mufti Mahdi Hassan (rahmatullahialay)
Hazrat Moulana Sulaiman Ahamd Nadwi (rahmatullahialay)
Hazrat Moulana Manzoor Nu'mani (rahmatullahialay)
Hazrat Moulana Syed Ataullah Shah Bukhari (rahmatullahialay)
Hazrat Moulana Mufti Mahmood (rahmatullahialay)
Hazrat Moulana Ghulamullah Khan (rahmatullahialay)
Hazrat Moulana Abdullah Darkhawasti (rahmatullahialay)
Hazrat Moulana Mawlana Hussain Ali (rahmatullahialay)
Hazrta Moulana Shams ul-Haq Afghani (rahmatullahialay)
Hazrat Moulana Khair Muhammed (rahmatullahialay)
Hazrat Moulana Tanveer Ahmad Khan (damat brakatuhum)
Fifth Generation
Hazrat Mufti Azam, Mufti Mahmoodul Hassan Gangohi (rahmatullahialay)
Hazrat Mufti Azam, Moulana Mufti Rasheed Ahmad Ludhyanvi (rahmatullahialay)
Hazrat Shaikhul Islam, Moulana Abul Hassan Ali Nadwi (rahmatullahialay)
Hazrat Moulana Mufti Abdush Shukoor Tirmidhi (rahmatullahialay)
Hazrat Moulana As'ad Madani (rahmatullahialay)
Hazrat Moulana Allamah Khalid Mahmood (damat barakatuhum)
Hazrat Moulana Allamah Safraz Khan Safdar (damat barakatuhum)
Hazrat Moulana Yusuf Palandri (damat barakatuhum) - student of Allamah Anwar Shah Kashmiri (rahmatullahialay)
Hazrat Moulana Qadi Mazhar Hussain (rahmatullahialay)
Hazrat Moulana Qadi Ahsan ullah Shujaabadi (rahmatullahialay)
Hazrat Moulana Saleem ullah Khan (rahmatullahialay)
Hazrat Moulana M. Abdullah Shaheed (rahamtullahialay)
Hazrat Moulana Zia ul-Qasmi (rahmatullahialay)
Hazrat Moulana Muhammad Umar Palanpuri (rahmatullahialay)
Hazrat Moulana Ibrahim Dewla (rahmatullahialay)
Sixth Generation
Hazrat Mufti Azam, Moulana Qadhi Mufti Abdur Razzak Khan Sahib (damat barakatuhum) - well I can't exclude my Shaikh can I?
Hazrat Mufti Azam, Moulana Mufti Rafi Usmani (damat barakatuhum)
Hazrat Mufti Azam, Moulana Mufti Taqi Usmani (damat barakatuhum)
Hazrat Muhaddith, Moulana Shaikh Yunus Janpoori (damat barakatuhum)
Hazrat Shaheed Moulana Mufti Yusuf Ludhyanvi (rahmatullahialay)
Hazrat Mufti Azam, Moulana Mufti Sa'eed Ahmad Palanpoori (damat barakatuhum)
Hazrat Moulana Ameen Safdar Okarwi (rahmatullahialay)
Hazrat Moulana Anzar Shah Kashmiri (damat barakatuhum)
Hazrat Moulana Qadhi Mufti Mujahidul Islam Qasmi (rahmatullahialay)
Taken from http://www.sunniforum.com/forum/showthread.php?32158-Palanpuri-Kandhalwi-Thanwi-Ludhianwi-Gangohi-Qasmi-Dahalwi-Usmani-amp-Jhangwi