Gemara

(Beraisa): If one had Bi'ah with his father, or with his father's brother, he is liable twice.

This can even be like R. Yehudah. He learns (extra) liability for Bi'ah with his father from a Kal va'Chomer. If one is liable (an extra Korban) for (Bi'ah with) his uncle, the relative of his father, all the more so he is liable for his father!

R. Yehudah holds like Abaye (76a), that Onshim Min ha'Din (we punish due to a Kal va'Chomer). Chachamim disagree, and learn from elsewhere.

Makos 2a (Mishnah): If witnesses testify that a Kohen is the son of a Gerushah (divorcee) and they were Huzmu, they receive 40 lashes.

4a (Mishnah - R. Meir): if Edim Zomemim testified that Reuven is liable to receive 40 lashes, they receive 80 lashes, 40 for "Lo Sa'aneh", and 40 for "Va'Asisem Lo Ka'asher Zomam."

Chachamim say, he receives only 40 lashes.

4b: Chachamim hold that "Lo Sa'aneh" is the warning for Edim Zomemim. R. Meir holds that it is "Veha'Nish'arim Yishme'u v'Yira'u v'Lo Yosifu".

5b (Mishnah): "Va'Asisem Lo Ka'asher Zomam La'asos l'Achiv" connotes that the Nidon is still alive.

(Beraisa - Beribi): If they did not kill, they are killed. If they killed, they are not killed. Ein Onshim Min ha'Din.

14a (Beraisa - R. Yitzchak): The Torah mentions Kares for Bi'ah with a sister, even though all Arayos are Chayvei Kerisus, to teach that it (and all other Chayavei Kerisus) are punishable by Kares, and not by lashes.

Chachamim learn from this that if one has Bi'ah with his sister, who is also the sister of his father and mother, he is liable for each of these.

Suggestion: R. Yitzchak learns this from a Kal va'Chomer. If one has Bi'ah with five Nidos in one Helam (i.e. he did not realize the Isur in between), he is liable for each woman. All the more so, when they are different Arayos, he is liable for each!

Rejection: He is liable for each Nidah, for they are different women! Rather, he learns from the end of the verse ("Ervas Achoso Gilah").

Chachamim learn from this that one is liable for a full sister, for Ein Onshim Min ha'Din (we cannot learn from liability for a half sister).

Question: What is R. Yitzchak's source to obligate for a full sister?

Answer: He learns liability from the Lav. Alternatively, he learns from the Reisha of the verse ("Achoso Bas Aviv Oh Vas Imo").

Chulin 115b (Beraisa - Isi ben Yehudah): A Kal va'Chomer forbids benefit from Basar v'Chalav. Orlah did not result from an Aveirah, yet it is Asur b'Hana'ah, and all the more so Basar v'Chalav, which results from an Aveirah!

Do not say that we cannot learn from Orlah, for it never was permitted. Chametz is Asur b'Hana'ah, even though it was once permitted!

Question: We cannot learn from Chametz, for which there is Kares!

Rishonim

Rambam (Hilchos Edus 20:2): If the Nidon was killed and afterwards the witnesses were Huzmu, we do not rely on a Kal va'Chomer to kill them. It says "Ka'asher Zomam", i.e. they did not yet do it. However, if the Nidon was lashed (and then they were Huzmu), the witnesses are lashed. If the money was transferred, it is returned, and the witnesses pay him.

Rebuttal (Ra'avad): This is wrong.

Ramban (Devarim 19:19): When two witnesses testify that Reuven murdered, and two other witnesses are Mezim the first ones, the Torah commands to kill the first ones. This occurred because Reuven is a Tzadik. If he were a Rasha, Hash-m would not have saved him from Beis Din - "Ki Lo Atzdik Rasha." If Reuven was killed, we assume that the first testimony was true. If he were innocent, Hash-m would have saved him - "Hash-m Lo Ya'azvenu v'Yado v'Lo Yarshi'enu b'Hishafto". Also, Hash-m would not allow righteous judges standing in front of Him to kill an innocent person - "judgment is to Hash-m, amidst judges He judges." This is based on the virtue of Yisrael judges, and Hash-m's guarantee that He agrees with them and is with them in judgment. This is why it says "the two men will stand in front of Hash-m."

Me'iri (Makos 3a DH Zeh she'Omru): Regarding Misah, the Ge'onim explain that since the witnesses schemed not at a time of heated controversy, and transgressed murder and false testimony, they are not worthy of atonement. Similarly, one who killed b'Shogeg is exiled, so he will get Kaparah, but not one who killed b'Mezid. I say that the primary reason is concern for disgrace of Beis Din. Killing the Edim Zomemim would publicize that Beis Din mistakenly killed the Nidon, and people will think that they did not interrogate the witnesses enough. The judges pursue other ways to properly punish the witnesses.

Magihah (59): The Rambam explains like the Me'iri in Moreh Nevucim 3:4. The Pnei Yehoshua, who says that the Abarvenel (Parshas Shoftim) says so, and also others.

Tosfos (115b DH Mah): We cannot learn from a Kal va'Chomer from Chametz that there is Kares for Basar v'Chalav, for Ein Onshim Min ha'Din.

Ritva (Makos 14a DH veha'Lo): How did the Gemara try to learn liability for a sister and aunt from a Kal va'Chomer? Ein Onshim Min ha'Din! We can say that regarding Korban, Onshim Min ha'Din. The Ra'avad says that since we merely learn to obligate for each, it is only a Giluy Milsa.

Aruch l'Ner (14a DH bi'Gemara): If for Korban, Onshim Min ha'Din, why did the Gemara ask what is R. Yitzchak's source to obligate for Bas Aviv who is Bas Imo? Ein Onshim Min ha'Din does not apply to Kares, like the Maharsha wrote. (I was unable to fiind the Maharsha- PF.) We do not punish Min ha'Din, lest the punishment does not help for the greater Aveirah, but Hash-m (who presides over Kares) knows! R. Yitzchak holds that there are no lashes for Chayvei Kerisus, so we must say that we ask about Korban! We can say that we asked why he learns that Kares exempts from lashes, and not like Rabanan, that Ein Onshim Min ha'Din, and Achoso obligates lashes for a full sister. However, Sanhedrin 54a is difficult. We say that Abaye and Rava argue about Onshim Min ha'Din. They must argue about Korban, for we cannot kill someone twice! Do not say that the Ritva said so only here, where the Isur is written and we need to learn only separate Korbanos from the Kal va'Chomer, but there we need to learn Kares, which is the source for Korban. All agree that we learn Kares from a Kal va'Chomer! I later saw that Shiyurei Keneses ha'Gedolah (OC Klalei Kal va'Chomer) says that R. Elyakim and R. Eliezer mi'Mitz hold that Onshim Min ha'Din for Kares and Misah b'Yedei Shamayim, but he himself disagrees. It seems that also Tosfos in Chulin disagrees. Why didn't they mention that Sanhedrin 54 proves that Ein Onshim Min ha'Din either for Korban or Kares? Since the Ritva holds that for Korban Onshim Min ha'Din, he must hold that Kares Ein Onshim. According to the Maharsha, for Kares Onshim Min ha'Din (for it is due to Hash-m), and it follows that there is a Korban for Shogeg. Halichos Olam holds that Ein Onshim Min ha'Din, lest we overlooked a refutation of the Kal va'Chomer. If so, we cannot bring a Korban (Chatas) for the same reason. I say that in Makos, after challenging the Kal va'Chomer, we conclude that one is liable for a sister and aunts when they are separate women. This is not a Kal va'Chomer from Nidah. Rather, it is the same Chidush, that one is liable for separate women even when the Isurim have the same name (they are all sisters).

Einayim l'Mishpat (Sanhedrin 54a:1): Ginas Veradim (Kelal 1:5 (Note: I did not find it there - PF) says that we learn only one level from a Kal va'Chomer, but not two. It suffices to learn Isur, but not Onesh. One can ask whether the Chiyuv Korban is a new Chiyuv, or if it follows from the Chiyuv for the Onesh. Even if it follows from the Chiyuv for the Onesh, perhaps we learn only one level from a Kal va'Chomer. However, if the Onesh is explicit and need not be learned from a Kal va'Chomer, we can learn Korban. The Rosh holds that even Kares is learned from a Kal va'Chomer, but this is unlike the Poskim.

Einayim l'Mishpat (Makos 5b:3): Also R. Yehonason (in Shitah Mekubetzes Bava Kama 4b) and the Or Zaru'a hold like the Ritva.