Dua- When waking up

1. Alhamdu lillaahil-lathee 'ahyaanaa ba'da maa 'amaatanaa wa 'ilayhin-nushoor.
 Praise is to Allah who gives us life after He has caused us to die and to him is the return.
Reference: Al-Bukhari, cf. Al-Asqalani, Fathul-Bari 11/113; Muslim 4/2083

2. Laa 'illaha 'illallahu wahdahu la shareeka lahu, lahul-mulku wa lahul-hamdu, wa Huwa 'alaa kulli shay'in Qadeer Subhaanallahi, walhamdu lillaahi, wa laa ;ilaha 'illallahu, wallaahu 'akbar, wa laa hawla wa laa Quwwata 'illaa billaahil-'Aliyyil-'Adheem, Rabbighfir lee.
There is none worth of worship but Allah alone, Who has no partner,His is the dominion and to him belongs all praise, and He is able to do all things. Glory is to Allah. Praise is to Allah. There is none worth of worship but Allah. Allah is the Most Great. There is no might and no power except by Allah's leave, the Exalted, the Mighty. My lord, forgive me.
Reference: Whoever says this will be forgiven, and if he supplicates Allah, his prayer will be answered; if he performs ablution and prays, his prayer will be accepted. Al-Bukhari, cf Al-Asqalani, Fathul-Bari 3/39, among others. The wording here is from Ibn Majah 2/335.

3. Alhumdu lillahil-lathee 'aafaanee fee jasadee, wa radda 'alayya roohee wa 'athina lee bithikrihi.

Praise is to Allah Who gave strength to my body and returned my soul to me and permitted me to remember him.

Reference: At-Tirmithi 5/473. See Al-Albani's Sahih Tirmithi 3/144.

4. Read the last ten ayas of Surah Ale-imran (190-200)

Reference: Quran Aal-Imran 3:190-200; Al-Bukhari, cf. Al-Asqalani, Fathul-Bari 8/237; Muslim 1/530

Fortress of the Muslim: Invocations from the Qur'an & Sunnah