The Talmud (Baba Metzia 59B) says, in the name of R' Elazar HaGadol, that 36 times in Torah we are warned against the wronging of a convert (46 if you count the times it says "because you were strangers in egypt" and the like - Tosafot). The reason given is because a convert has a strong inclination for evil, and you do not want to drive him back to his old ways.
I just came across the Rimzei Baal HaTurim to Devarim 1:1 (printed in most Chumashim). There, he says that warnings against both Idol Worship and Wronging a Convert are mentioned 48 times in the Torah. (the Artscroll Baal HaTurim Chumash notes the discrepancy between the Talmud and the Baal HaTurim, but does not explain why).
This answers the question, but the discussion the question has come up whether there is a difference between mentioning something in the Torah, and being commanded about it in the Torah.
I don't know the answer, but right before the Gemara bring R' Elazar HaGadol's statement it quotes the Rabbis, who conclude that if one oppresses a convert he transgresses 3 prohibitions and if he wrongs a convert he transgresses 3 prohibitions.
I guess there are two ways of looking at this. The first way is that there is a difference between a warning from the Torah and a prohibition from the Torah (and R' Elazar and the Rabbis are not arguing).
The other way of looking at it is that R' Elazar is arguing with the Rabbis and hold that when one wrongs a convert he transgresses 36 (or 46) prohibitions.
It is worthwhile to point out that the Kaftor V'Perach writes that a grandchild of the Rambam told him that while the Rambam was in Egypt he would sign his letters, "Rabbi Moses ben Maimon, from Spain, who every day transgresses three commandments in the Torah [not to live in Egypt]." (see here, here, and here)
The Mechilta (Shemos 14:13) brings the three places where we are told not to return to egypt:
"You shall not return..." (Devarim 17:16)
"... for as you have seen Egypt today, you shall never see them again" (Shemos 14:13)
"Hash-m will return you to Egypt in boats, on the path of which I said to you, 'Never again shall you see it'" (Devarim 28:68)
It seems that the 3rd mention is not a commandment against going to Egypt, but a mentioning of the prohibition previously stated. Yet it is still considered a prohibition. This would seem to indicate that every time a prohibition is mentioned it is considered an added prohibition (even though it is only 1 of the 613 commandments)
See Rambam Sefer Himitzvos Negative Mitzva 179, where the Rambam first brings the opinion that for eating a Sheretz Hamayim one gets 6 sets of lashes, but then rejects that, since 3 of the lashes are for a singe prohibition, which goes against the rule in the Talmud that a person cannot get more than one set of lashes for every prohibition he transgresses.
The Rambam then says, "Have you seen those who propose this erroneous principle dictating two sets of lashes for a person who wears shatnez, since there are two prohibitions? I have not seen them say such a thing, and they would consider it strange if anyone else did."
All this would seem to indicate that it is possible for the same thing to be prohibited many times, but a person is only punished once. It would seem however, that he is still considered to have transgressed many prohibitions (as indicated from the way the Rambam would sign his letters).