Many people are naturally inclined to rub their eyes upon waking in the morning, but this should be avoided. The Shulhan Aruch (Orah Haim 4:3) writes that one should not touch any of the openings to his body – his mouth, his nostrils, his ears, or his eyes – in the morning before washing Netilat Yadayim.
Hacham Ovadia Yosef cites the Solet Belula as asserting that the Sages forbade this because it could lead to spiritual harm – meaning, touching one's eyes could cause spiritual "blindness," an inability to "see" and understand Torah, and touching one's ears could affect his spiritual "hearing," his ability to listen and absorb Torah wisdom. However, Hacham Ovadia disputed this explanation, noting that it fails to account for the prohibition against touching one's mouth or nose before washing. Hacham Ovadia therefore adopted the more straightforward understanding, that the impurity on a person's hands in the morning could cause physical harm if they come in contact with the orifices on one's body.
This prohibition applies also to the openings of the body in one's private areas.
It is forbidden to touch the openings only with one's fingers; one may touch them with the palm of one's hand.
Numerous Poskim – including the Ben Ish Hai, Mishna Berura, and Kaf Ha'haim – rule that it is forbidden in the morning to touch even the areas around the eyes, nose, ears and mouth. One who needs to do so should touch them indirectly, with a cloth or tissue. However, Hacham David Yosef, in Halacha Berura, writes that if one has a particular need, and no cloth is available, he may rely on the lenient view that allows touching the area around the openings to the body.
The Yalkut Yosef rules that if a person has a particular need – such as if he suffers from an eye infection, and cannot wait to rub his eyes until after Netilat Yadayim – then he may rub his eyes, relying on the Rambam's view that harmful spirits do not exist nowadays. Rav Yisrael Bitan, however, disagrees, noting that the Rambam's view can be relied upon only in situations of great need, and in this case, one has the option of using a tissue or cloth, or waiting just a few moments until after Netilat Yadayim. One may be lenient in such a case, Rav Bitan rules, only if he is in great distress and has no tissue or cloth available, or if he had gone to sleep after halachic midnight, as we may take into account the view that the harmful spirits descend upon the hands only if one had gone to sleep before midnight.
This Halacha does not apply to the impurity that descends upon the hands in the restroom. Therefore, after leaving the restroom, it is permissible to touch the openings to one's body even before washing Netilat Yadayim. However, one should refrain from touching food or beverages after leaving the restroom until he washes his hands. If he did touch food or a beverage before washing, then the food or beverage remains permissible, but if it can be rinsed, it should be rinsed three times before being consumed.
One should not touch Torah books in the morning before washing Netilat Yadayim.
It is permissible to smoke a cigarette in the morning before washing Netilat Yadayim. One should not, however, smell snuff in the morning before washing Netilat Yadayim. If one feels a need to smell snuff immediately upon waking, he may, though he must ensure not to touch his nostrils.
Incidentally, Rav Haim Palachi (Turkey, 1788-1868) ruled that one may not smell snuff in a cemetery because there are impure forces in graveyards. Hacham Ovadia Yosef, however, disagreed, and maintained that there is no concern. Clearly, it is forbidden to eat in a cemetery, because one may not perform Misvot in the presence of the deceased, and this includes reciting Berachot over food. (Interestingly, Rav Haim Palachi also ruled that one may not smell snuff after leaving the restroom, while in a public bathhouse, or after taking a haircut or cutting one's nails, until washing Netilat Yadayim.)
Summary: After waking in the morning, one must ensure not to touch any openings in his body – his ears, eyes, mouth, nostril or private areas – until washing Netilat Yadayim. If one must rub his eyes or a different opening, he should do so with a tissue, cloth, or a part of his hand other than his fingers. One should not touch Torah books in the morning before washing Netilat Yadayim.