None, nonbelievers and believers both commit good and bad deeds, at least in action. Faith is required for an action to be good when it is good.
Nonbelievers may give charity, help the needy, love others for the sake of it and refrain from cruelty and injustice. They may spread peace as well. But, these are not necessarily rewarded by Allah or even considered good in His sight. What is good is whatever is good done for the sake of Allah. This is the separation between the good deeds done by believers and nonbelievers.
To understand this, think of animals. They love their children, and they love others in their groups and even fight for each other. They feed each other and they also work together. This does not mean that human who do the same are any different, they are still very much animal-like. Thus, only those people who do such deeds for the sake of Allah can ever be rewarded for what they do by Him. Their deeds are considered good because they have attributed what they do to Allah.
To then understand how a believer does their actions for the sake of Allah, the explanation is that when we do things we first say Bismillah, otherwise, what we do is cut off from all goodness since it is not done for Allah's sake. There is a Hadith which says this very thing. Think about our Niyyat for Salat, we recite our intentions and say that our prayers all belong to Allah, making our intention for Him only. Thus, this is another reason why intentions are important in Islam. Therefore, tell your Atheist friend to not think of morality as inherent in everyone, morality is whatever is done for the sake of Allah. Islam is about intention, and your Atheist friend should also understand that every action is preceded by an intention. The intentions which are for the sake of Allah are the highest and most deserved intentions and there is nothing which can outdo that. That defines morality, and thus it is based upon our deeds being for the sake of Allah only.
Otherwise, if we do something for ourselves or because we felt like it and thought it was good, then morality has no definition except that we do as we like because we feel it is right at the time. Some people think killing can be moral, others don't. Who is right? There is no accepted definition of morality amongst Atheists except that whatever we do we feel is right and which does not cause harm to others is right. But this is empty, because it fails to consider that there are flaws in how we think we affect others. Humans cannot predict everything. Thus, only Allah can save us from this and give us laws which comprehend all aspects of life that nullifies harm altogether. Only He can keep us from harming each other by His laws. Humans are foolish to think they can govern themselves and leave Allah out of it.
As for,
I should like to note that whether evil is done in the name of religion or not, it remains an evil. This argument that religion is flawed because people commit crimes in its name is silly. If Muslims are claiming to kill in the name of Islam, then they are not following Islam and the rest of the Muslims disagree with them and even resist them.
As for violence in the name of Allah, it is Haram to do so unless everything is in accordance with Allah's Laws. No Muslims can make up the Laws of Islam on their own and take the law into their own hands. Atheists do not understand how the religion works, so tell him that those who claim to do acts of violence and killing in Allah's Name have nothing to do with Islam because disobedience to Allah is Kufr, and any Kafir is not a Muslim. Simple as that. Actions of Kufr render a Muslim a Kufr at that time. Killing cannot be done unless it is because one has to kill someone who murdered another person. There is a specific Hadith on this. Tell him this Hadith:
Narrated Ibn 'Umar: Allah's Apostle said, "A faithful believer remains at liberty regarding his religion unless he kills somebody unlawfully." (Book #83, Hadith #2)
(Sahih Bukhari)
Sorry for the long answer. But I hope what I told you makes sense and answers your question so you have a peace of mind and can answer the Atheist who asked you these questions.
