Sunnah And Nafls Salaah

Rules of Sunnah-e-Maukida and Ghair Maukida
There are many Sunnahs which are regarded as Maukida, whereby it has been regarded as important in Shariah and to miss it even once without reason is worth reprimanding, and to make a habit of missing them would mean being a wrongdoer (Fasiq) who's giving oath would not be counted and is worthy of hell.

To miss it is close to Haram and those who miss it have a risk of not being interceded on the day of judgement.

Sunnah-e-Maukida is sometimes also referred to as Sunun-e-Hidaya. Many Sunnahs are Ghair Maukida and are sometimes referred to as Sunun-e-Zawa'id and it's importance has not been defined in Shariah and sometimes is quoted as Mustahhab.

Nafl are those actions which by doing would gain reward and to miss carries no punishment and there is no harm in missing.

Salaah which is Sunnah-e-Maukida
C141.1 The Sunnah-e-Maukida are these;
a) The first two Rakats of Fajr, before the Fardh Salaah
b) The first four Rakats of Dhuhr before the Fardh Salaah and the two Rakats of Dhuhr after the Fardh Salaah.
c) The two Rakats after the Fardh Rakats of Maghrib
d) The two Rakats of 'Isha after the Fardh Rakats.
e) The first four Rakats before Fardh of Ju'ma and the four Rakats after Fardh and it is better also to pray the two Rakats additionally after Fardh [Guniya, Hidaya].

The most important Maukidah is the Sunnahs of Fajr, upto the extent that many Ulema regard them as Wajib. Therefore they cannot be prayed without reason whilst sitting or on a vehicle or moving car [Fatahul Qadir etc.].

Rules of missing Sunnahs 

If the Fajr Salaah became Qadha and you prayed them before midday then also pray the Qadha for the Sunnahs otherwise don't. Except for Fajr if all other Sunnahs became Qadha, then there is no Qadha for them. 

If you missed the first Sunnahs of Dhuhr or Ju'ma and prayed the Fardh Rakats then if there is time pray the Sunnahs after and it is better to pray them after the normal Sunnahs that are prayed after the Fardh Salaah [Fatahul Qadir, Bahar].

If the Sunnahs of Fajr are not prayed and the Fardh Salaah is prayed then do not pray them until after sunrise as Qadha as it is better to pray them after sunrise and it is not allowed to pray them in this situation before sunrise [Radd-ul-Mohtar, Bahar].

It is Sunnah to pray in the Sunnahs of Fajr, in the first Rakat 'Qul Yaa Ayyuhal Kafiroon' and in the second 'Qul Huwallaho Ahad'.

 When Nafl is allowed
It is not allowed to start any Nafl or Sunnah once Jamaat has started. The only exception is the Sunnahs of Fajr and the rule is you must start them even if the Jamaat has started as long as you are aware that you can finish the Sunnahs and join the Jamaat even if it is in the last Qaidah. You must pray these Sunnahs separately away from the rows of Jamaat as to pray them in the same row as the Jamaat is not allowed.

If you are aware that if you pray Nafl or Sunnah then you will miss the Jamaat, then it is not allowed to start the Nafl or Sunnah.

Mustahhab Salaah
Four Rakaat Salaah before 'Isha and 'Asr and four Rakats after 'Isha all with one Salaam is Mustahhab. It is also the case if you pray two Rakats after 'Isha then the Mustahhab will be fulfilled. It is also Mustahhab to pray four Rakats after Dhuhr. It is quoted in the Hadith that those who pray these will have the fire of hell made Haram for them.