There are some 15 words in the Tanach which are nakud (dotted). The most probable explanation is that they were inserted to call attention to some important homiletical teaching in connection with the words, but possibly they indicate that the words or letters were doubtful and are to be deleted, presumably when Elijah comes and resolves the various scribal disagreements that have sprung up. Ezra is hedging his bets saying that if Elijah says ‘why have you written these words’ he will reply ‘I have placed dots over them’ and if he says ‘you have written them correctly’ then he will remove the dots! (Avot d’Rabbi Natan 30b).
10 of these appear in the Torah mostly in Genesis or Numbers, though the last being in Deuteronomy being the most extravagant with no less than 11 dots over three consecutive words.
1. Gen. 16:5 - u’veynecha (let God judge between me [Sarah] and between you [Abraham]) has one dot above the yud. teaching that this issue was restricted to Sarah reproaching Abraham only on the matter of Hagar and not others. Alternatively Sarah does intend her words against any who stir up strife between her and her husband as words between them should be of no concern to others. (ARN 30b)
2. Gen. 18:9 - eylav (and they said to him, where is Sarah your wife) has three dots over the aleph, yud and vav. This is because these heavenly creatures actually knew very well where she was they asked a rhetorical question specifically to him (i.e. Abraham) out of courtesy. (ARN 30b)
3. Gen. 19:33 - uv’kumah (and he [Lot] was not aware of her lying down and of her gettingup) has one dot over the second vav. The Ba’al Haturim says this is to teach us that Lot’s daughter lay with her father before vav i.e. six hours of the night had passed and thus he was sleeping soundly when she got up. And he was not aware of when his youngest daughter arose but he was when his eldest did. (ARN 34:4), but the Talmud (Nazir 23a) and Bereshit Rabbah 51:8 say that the dotted vav indicates that he was unaware of her lying down but was aware in reality of her getting up, but acted as if he did not. With this in mind he should have not have let his daughters ply him with drink a second night, but he did.
4. Gen. 33:4 - vayishakehu (Esau ran towards him [Jacob], embaced him, fell upon his neck, and kissed him and they wept) has six dots, one over each letter. This is perhaps the most famous of the dotted letters as it is explained by the Rabbis that it intimates that Esau did not kiss his brother Jacob, rather he bit or at least intended to (Ba’al Haturim) bite him the same Hebrew word but a completely different meaning showing that Esau remained insincere in his reconciliation with Jacob and the dots indicate in some sense that the word is not fully there, as Esau’s intention contradicted his action. Alternatively he did not kiss him with sincerity (ARN 30b) or according to R. Simeon b. Eleazar this was the only time it was sincere and all other times it was insincere.
5. Gen 37:12 - et (Now his [Joseph’s] brothers went to pasture their father’s flock in Shechem) has two dots, one over each letter, teaching that they did not go to feed the flocks but to eat drink and indulge in pleasures, the et suggesting more on the list of actions. (ARN 30b)
6. Num. 3:39 - v’aharon (All that were numbered of the Levites whom Moses and Aaron numbered) has five dots, one over each letter, teaching that Aaron was not included in that census even though he was a Levite.
7. Num. 9:10 - r’chokah (or be in a journey far off) has one dot over the heh. The explanation to this is given by R. Jose in Pesachim 9:2 that far off doesn’t actually mean far away, but only [as far off as] beyond the threshold of the temple court.
8. Num. 21:30 - asher (and we have laid waste even to Nophah, which reaches to Medeba) has one dot over the resh. This teaches that they destroyed the only the people [who were idolators] and not the lands. Others say they destroyed the lands and not the people.
9. Num. 29:15 - v’isaron (and a separate tenth part) has one dot over the second vav, teaching that there was only to be one tenth-measure, even on occasions when three tenths had to be used.
10. Deut. 29:28 - lanu u’l’vaneynu ad (unto us and unto our children until) has eleven dots one over each letter of the three words except the last letter dalet. This teaches that God did not punish them for any sin until they had crossed the Jordan.
The most interesting use of dots, however, is to be found in the Psalms 27:13 where the word luleh (if I had not believed to look upon the goodness of the Lord) has dots both above (three) and below the word (two).
Sources: Avot d’rabi Natan 30b, parallels in Sifre to Numbers 9:10, Midrash Rabbah Numbers 3:13, and Soferim 6.