A bit of a necropost, but people still read this, as it's one of only a few conversations about it online, so here goes.
BOOK SPOILERS AHEAD:
I'm a bit shocked that nobody here seems to know what Geralt's first wish was, especially since it was pointed out so explicitly in the book. It wasn't for the djinn to 'leave Dandelion alone' or for him to 'shut his mouth', as others have suggested. To quote the book, the rough translation of what he commanded the djinn to do while holding the sigil was "get out of here and go fuck yourself". He didn't know that's what he was commanding it to do, because he didn't speak the language, but that's what he commanded the djinn to do and that's exactly what it did (although we were spared from seeing it fulfill the second part of the command). The book is very, very clear that this was what the wish was; the sigil heated up right after he said that, showing that it had activated, and most importantly, Geralt insisted that the priest translate the command even though it was improper to ask because at that point he knew that it was he who had wished, and that it was that particular phrase, so he had to know its translation to verify (and indeed, it was true). Check pages 280 and 330 of the standard paperback edition.
So, wish 1, to the djinn; "Get out of here and go fuck yourself".
Everyone knows what wish 2 was, poor sadistic guard. Bald people always suffer. One of the last acceptable discriminations, really.
As for wish 3: yayodeanno definitely had it right when he said that we cannot know for sure what it was. That's part of what makes Sapkowski such a great writer: leaving certain things to the imagination. There are, however a few things that people seem to think that it was that it COULD NOT have been, given the evidence:
a) For Geralt and Yennefer to have a baby together. This is sort of clever, since the djinn after fulfilling this wish wouldn't be able to kill them, at least not for awhile, and whatever his wish was certainly had the effect of preventing the djinn from killing them. It is, however, simply untrue. First off, Sapkowski explicitly denied that this was the wish in an interview, which is enough to settle it, but anyone could have come to that conclusion by knowing who Geralt is: he would absolutely never force his (physically impossible) offspring on a woman without asking for her consent, even if it would save her life. He is not that sort of man, and if you don't agree with that statement you have clearly not read the book.
For Yennefer to fall in love with Geralt. This is very popular, but entirely impossible for it to have been what he wished, for two reasons. The first is, as stated above, that Geralt would never force his love on someone else. That would directly conflict with the code of conduct and morality which is the centerpiece of the book. The second is that this would do absolutely nothing in protecting either of them from the djinn, which at that point was out for Yennefer's blood and possibly Geralt's as well. Had he wished that (essentially amounting to rape of the mind, incidentally, which we know he wouldn't do), the djinn would have granted it and then happily killed her (and possibly him). Therefore, the popular "for Yennefer to love me" wish cannot possibly be correct.
c) For Yennefer to forget that she had ever been a hunchback. I suppose a few people think this because it was on his mind shortly before he made the wish, but it's impossible for the reasons above: it would not have prevented the djinn from killing them, and mind-controlling Yennefer would have been a reprehensible act (although she did do it to him). Beyond these, however, are two infallible additional reasons: 1) she remembers that she was one just fine in a future book (sorry, very minor spoiler there) and 2) she wouldn't have known what his wish was, having had to forget it because the very wish would have reminded her of it, and yet she does remember. So four(!) reasons that could not have been it.
All we can know is that Geralt's Last Wish, whatever it was, had the effect of both protecting them from the djinn and "binding their fates" together, as the priest suggested. Remember, also, Yennefer's reaction to it: that it was something so powerful that she doubted that there was any Force in Nature that could grant it, but that if there was, that Geralt had condemned himself to her.
Given Sapkowski's fondness for fairy tales and all of these things, I like to think that Geralt's wish was for both of them to live happily ever after. But as long as your guess abides by the rules and exceptions listed above, then it's every bit as good (or better) than mine. Peace.