Praise be to Allah.
It was narrated that Hudhayfah ibn al-Yamaan (may Allah be pleased with him) said: I prayed with the Prophet (blessings and peace of Allah be upon him) one night. He started to recite al-Baqarah, and continued to recite until he completed one hundred verses, and I thought that he would bow. Then he continued until he had recited two hundred verses, and I thought that he would bow. And he continued until he completed it, and I thought he would bow. Then he started to recite an-Nisa’, and he recited, then he bowed, and his bowing was as long as his standing, and he said whilst bowing: Subhaana Rabbiy al-‘Azeem (Glory be to my Lord Most Great). Then he prostrated, and his prostration was as long as his bowing, and he said whilst prostrating: Subhaana Rabbiy al-A‘laa (Glory be to my Lord Most High). When he came to a verse that spoke of mercy, he prayed for mercy; when he came to a verse that mentioned punishment, he sought refuge with Allah from it; and when he came to a verse that glorified Allah, he glorified Allah.
Narrated by Ahmad in al-Musnad (23261) and by Ibn Khuzaymah in as-Saheeh (586).
Such was the practice of the Prophet (blessings and peace of Allah be upon him) when reciting Qur’an and interacting with the meanings of the verses. This is a type of reflecting and pondering the meaning. As-Suyooti said: It is Sunnah to recite with reflection and pondering the meaning. That is the greatest goal and most important aim, by means of which hearts find comfort and illumination.
How that is done: the worshipper should focus on the meaning of the words he is uttering, so that he will think of the meaning of each verse, reflect on the commands and prohibitions, and affirm to himself that he will comply with them. If there is something concerning which he fell short in the past, he should apologize and seek forgiveness. If he comes to a verse that mentions mercy, he should feel hopeful and ask Allah for it; if he comes to a verse that mentions punishment, he should feel concerned and seek refuge with Allah from it; if he comes to a verse that glorifies Allah, he should declare Allah to be above all shortcomings and glorify Him; if he comes to a verse in which there is a supplication, he should turn to Allah and ask of Him.
End quote from al-Itqaan (1/369).
With regard to interacting with the meaning of the verses in general terms, there is nothing wrong with that, such as when a person understands the meaning of a verse and feels moved by it, so he says Subhaan Allah (Glory be to Allah) or similar words which show that the verse has had an impact on him, saying words that are appropriate to the context and meaning of the verse.
But that is on condition that he does not burden himself with doing that (rather it should come naturally). For we are forbidden to go out of our way to do something that we find burdensome. Moreover, obliging ourselves to say words, even if it is glorification of Allah (tasbeeh) or supplication (du‘aa’), every time we come to a verse could interrupt the attention of the one who is listening to the one who says that, if he is listening to the recitation of someone else, or it could interrupt the flow of his recitation, if he himself is the one who is reciting.
With regard to interacting with the meanings of the verses in prayer, Shaykh Ibn Baaz said: The best is to remain silent and listen attentively, when the imam is reciting in Maghrib, ‘Isha’ and Fajr, or in Jumu‘ah. The best is to remain silent and listen attentively, so you should not say tasbeeh when hearing the verses that mention glorifying Allah or proclaiming His oneness, and you should not say salawaat when a verse mentions the Prophet (blessings and peace of Allah be upon him), because Allah says (interpretation of the meaning): “So when the Qur'an is recited, then listen to it and pay attention that you may receive mercy” [al-A‘raaf 7:204]. So the best is to listen attentively. But if one sends blessings on the Prophet, or says Subhaan Allah when the names of Allah are mentioned, there is nothing wrong with that, although it is better not to do it, because what is narrated from the Prophet (blessings and peace of Allah be upon him) is that when he recited in a prayer in which recitation is done out loud, he did not pause when he came to a verse that mentions mercy, or a verse that contains a warning, or a verse that mentions the names and attributes of Allah. Rather he would carry on reciting. Therefore it is better for you to listen and not pause or say anything when the imam comes to these verses when he is reciting, or for you to do that when you are reciting in an obligatory prayer.
In the case of supererogatory prayers, however, the matter is broader in scope, such as when praying tahajjud at night and the like. When you are reciting, you may pause at a verse that mentions mercy and ask Allah for mercy; and at a verse that mentions a warning and seek refuge with Allah; and at verses which mention the names of Allah and glorify Him; and at verses which mention the Prophet (blessings and peace of Allah be upon him) and send blessings on him, and so on. This also applies if you are praying behind an imam in prayers such as Taraweeh and qiyaam in Ramadaan; if the imam pauses to offer supplication, you may offer supplication; or if he pauses to send blessings upon the Prophet, you may also send blessings upon him. But if he carries on reciting, you should keep quiet and listen attentively, because you are enjoined to listen attentively.
End quote from Fataawa Noor ‘ala ad-Darb, ash-Shuway‘ir (12/351).
Because this is something that is narrated as a Sunnah practice, to ask for mercy when coming to verses that mention mercy, and seeking refuge with Allah when coming to verses that mention punishment, and glorifying Allah when coming to verses that mention glorifying Him, then it is something that is undoubtedly prescribed, outside of prayer.
When one is praying, however, it is prescribed in general terms, although the scholars differed as to whether that applies only to the supererogatory prayers, because that is what is mentioned in the Sunnah, or whether it may be applied by analogy to the obligatory prayers too, which is the view favoured by Shaykh Ibn Baaz and other scholars, as has been explained previously on our website.
As for going beyond that, and working out a supplication for every verse, what appears to be the case is that this is not prescribed, especially in the prayer, because of what it involves of overburdening oneself, interrupting the flow of recitation and not listening attentively to it.
And Allah knows best.