Gemara

(Rav Chelbo): I once saw that Rav Huna wanted to sit on a bed on which a Sefer Torah was resting. He stood up a barrel and put the Sefer Torah on it, and then sat on the bed.

He holds that one may not sit on a bed on which a Sefer Torah rests. He argues with Rabah bar bar Chanah;

(Rabah bar bar Chanah citing R. Yochanan): One may sit on a bed on which a Sefer Torah rests;

Question: A case occurred in which R. Elazar realized that he was sitting on a bed on which a Sefer Torah rests. He sat on the floor and was grieved like one bitten by a snake!

Answer: That is wrong. Really, he realized that the Sefer Torah was on the floor!

Mo'ed Katan (25a): When Rav Huna died, they thought to put a Sefer Torah on his bed.

Rav Chisda: Something that he forbade in his lifetime, will we do so to him in his death?!

Berachos 18a (Beraisa): One may not put a sack of bones (of a Mes) on a donkey and ride on them, for this disgraces them. If he is afraid of Nochrim or bandits, it is permitted.

The same applies to a Sefer Torah.

Question: Does this refer to the Reisha (that one may not ride on it) or to the Seifa (one may ride on it to protect it from bandits)?

Answer: It cannot refer to the Reisha. We need not teach that we are not more lenient about a Sefer Torah than about bones! Rather, it refers to the Seifa. The same Heter applies to a Sefer Torah.

Yerushalmi (Berachos 3:5): One may not sit on a bed on which a Sefer Torah rests. If the Sefer was on something else, it is permitted.

(Rav Huna): The matter must be a Tefach (high).

(R. Yirmeyah): It can be any size.

Rishonim

Rif (Berachos 11a): Just like we said about bones, the same applies to a Sefer Torah. If he was afraid due to thieves or bandits, he may put it on the donkey on which he rides.

Rosh (3:7): If one is afraid of thieves or bandits, he may ride on bones. He may cast them in back of himself on the donkey. The same applies to a Sefer Torah. Even if you thnk that it is forbidden for a Sefer Torah, it is permitted for Nevi'im and Kesuvim. However, it seems that we permit even for a Sefer Torah. The Seifa permits not only for thieves and bandits. Obviously, it is better to disgrace a Sefer Torah and not hand it over to thieves and bandits. Rather, it was taught also for the inference from the Reisha, that one may cast them in back of himself. The Yerushalmi explicitly says so. The Rif connotes that Sefer Torah was taught only for the Seifa (but one may not put them on the donkey if he does not fear).

Ma'adanei Yom Tov (400): The Yerushalmi permits rising with Seforim on a donkey. If it does not permit a Sefer Torah, it must permit Nevi'im and Kesuvim. What other Seforim could it refer to?

Note: Gitin 60a mentions that R. Yochanan and Reish Lakish read in a Sefer of Agadata, but the Beraisa cannot refer to this, for it was not well known. (The Gemara proved from this that Chachamim may permit Isurim for a great need, e.g. to write oral Torah!) Gitin 60a and Ma'adanei Yom Tov support the opinion that the Mishnah was not written in the days of Rebbi.

Rambam (Hilchos Sefer Torah 10:6): One may not sit on a bed on which a Sefer Torah rests.

Ra'avad: If the Sefer Torah was on a place a Tefach high, it is permitted. The Yerushalmi says so.

Mordechai (Hilchos Ketanos 961): It seems that the Halachah follows R. Yochanan, for Rav Huna was Rav's Talmid, and the Halachah follows R. Yochanan against Rav. Further, even Rav Huna's Talmidim did not hold like him, like it says in Mo'ed Katan. The Ri says that even if one sits on a bed even (at the same level) with a Sefer Torah it is permitted, for we do not distinguish (and say R. Eliezer was stringent in this case). Rather, every case is permitted. The Yerushalmi says that one puts a box full of Seforim at the head of the bed, but not at the foot of the bed. R. Bun says that the bed must be 10 Tefachim tall, and the ropes of the bed do not touch the box. They put a Sefer Torah on the bier of Melech Chizkiyah. We must say that a Navi authorized this, or it is because he spread Torah in Yisrael.

Mordechai (Berachos 59, according to the Hagahah): If one has a big sack of Seforim or bones of a Mes, if he fears, he may ride on them. He may cast them in back of himself even if he does not fear. The Yerushalmi says so.

Tosfos (Mo'ed Katan 25a DH v'Chaf): They did not put the Sefer Torah higher than Rav Huna. This shows that even if it is higher, it is forbidden.

Beis Yosef (YD 282 DH v'Chasvu): R. Mano'ach says that the Yerushalmi did not resolve how much higher the Sefer Torah must be. Some rule stringently, e.g. the Ra'avad, who requires a Tefach. I say that it is proper to be stringent and require 10 Tefachim, or at least three Tefachim, for less than this is not considered high at all.

Shach (282:8): Ten Tefachim is Midas Chasidus. Letter of the law, one Tefach suffices, like the Yerushalmi and the Poskim that the Beis Yosef brings.

Poskim

Shulchan Aruch (YD 282:7): One may not sit on a bed on which a Sefer Torah rests.

Beis Yosef (DH Asur): The episode in which Rav Huna did not sit on a bed until he removed the Sefer Torah from it is brought in Mo'ed Katan and Menachos. Even though in Menachos it says that Rabah bar bar Chanah disagrees, the Tur rules stringently about honor of the Sefer Torah. Also, Rav Huna acted in practice, and the others did not do an act unlike him. Semak rules like this, and it seems that the Ra'avad agrees. Mordechai and Tosfos (Menachos 32b DH Amar) rule like R. Yochanan. Since the Rambam, Ra'avad, Semak and Tur forbid, and also Tosfos in Mo'ed Katan, R. Mano'ach, R. Meshulam, and the Yerushalmi, we follow them.

Gra (17): Even though elsewhere the Rambam rules like R. Yochanan against Rav Huna, here he followed the Yerushalmi, like he often does.

Rema: All the more so one may not put a Sefer Torah on the ground. The same applies to other Seforim.

Bedek ha'Bayis: R. Yerucham says that a bag full of Seforim is like a Sefer Torah for this. The Yerushalmi equates them.

Beis Yosef (DH v'Chosav): R. Mano'ach says that some say that we are stringent only about a Sefer Torah, but not for other Seforim. It is good to be stringent. This does not refer to the time of (learning in) the Beis Medrash. At the time of the Beis Medrash, if there is sparse room for Talmidim, one may sit even with Seforim and Perushim (on the same bench). R. Meshulam used to do so. When not in the Beis Medrash, he was particular that the Sefer be on top of something else of any size. Orchos Chayim says that one should not be lenient about this, lest it look like he disgraces the honor of Seforim.

Teshuvas Rema (34): One who rides on a donkey with a Sefer Torah puts it in front of himself. If he is afraid of Nochrim or bandits, he may ride on it. The Poskim and Tur rule like this. One may not even sit on a bed with Seforim, and all the more so one may not sit on Seforim! Some distinguish between a Sefer Torah and Seforim, the way some say that the Rosh (Berachos 3:55) distinguishes regarding marital relations in front of Seforim. Here, there is no difference. Seforim are more Kodesh than bones of Mesim. For this, Seforim are like a Sefer Torah, like the Mordechai says. I see that Seforim are more Kodesh than bones. One may have relations in a house with bones, but not in a house with Seforim, unless they are in a Kli within a Kli.

Teshuvas Rema: We should say that since the Seforim are in a box, this is its own Reshus! It seems that we do not distinguish this way. One may not put Tefilin under his head, and all the more so not under his feet (Berachos 23b), even though they are in a Kli in a Kli. We do not say that the Kli interrupts. We know that Seforim are more Kodesh than Tefilin. One must hold a Kodesh item when taking a Torah oath. Poskim say that Tefilin suffice only for a Chacham. If one spread a garment over a box, this is called a Kli within a Kli. This shows that a chest is called only one Kli, unless it is so big that it is a Reshus by itself and it is not considered a Kli. Perhaps our Seforim, which are not in Ashuris characters (those used in a Sefer Torah), are less Kodesh. Perhaps the Isur to write oral Torah was only in Ashuris. Perhaps a Kli separates for our Seforim. This requires investigation.

Taz (4): The Rema learns from here that one may not sit on a box with Seforim. He asked why the box does not separate, and concluded 'this requires investigation.' I say that we learn from Eruvin 30b. Tana'im argue about whether a moving Kli that holds 40 Sa'im blocks Tum'ah. The Halachah follows Rebbi, that it does not. All agree that a smaller Kli does not block Tum'ah. Here, putting a Talis over the box would not permit sitting on it, even though this helps for relations, since even a big box is considered movable and does not permit. We forbid (Sa'if 3) riding on a donkey with a bag of Seforim, i.e. even if there are many bags one on top of the other. The only Heter is if they are even with his heart. This is because sitting on them is a great disgrace. If it is nailed to the wall, it is permitted.

Rebuttal (Nekudas ha'Kesef): Also the Rema learned from Tum'ah. Here is different! There, since it is not an Ohel, it is a Kli. A Kli does not shield from Tum'ah, because it itself becomes Tamei. The Rema only learned that if for Tum'ah it is not a Kli, all the more so here it is not a Kli. If it is a Kli for Tum'ah, we cannot learn to here. One cannot learn from Sa'if 3, in which he weighs down on the Seforim. Tosfos (32b DH Asur) says that the Yerushalmi forbids sleeping on a bed with Seforim. Piskei Tosfos says that sleeping is more stringent, lest he come to pass gas or have relations. The Rema was unsure, for perhaps our Seforim are less Kodesh.

Note: Tosfos says that the Yerushalmi forbids under the feet, but permits under the head!

Bach (OC 171:2): If a box is of hard wood and it does not sag when one sits on it, he may sit on it even if it is full of Sifrei Kodesh.

Bechor Shor (Eruvin 30b, cited in R. Akiva Eiger and Pischei Teshuvah 8): Rashi (Gitin 8b) says that Rebbi holds that a big Kli is an Ohel, but only when it is stationary. The Rambam, Ra'avad and Tosfos in Chagigah and Nazir agree; Tosfos in Eruvin holds that it is never an Ohel. One may rely on the Bach in pressed circumstances, as long as the Kli is not designated for the Seforim, especially if there are also other things in the box, for then it is not Batel to the Seforim. One should be stringent if a Sefer Torah is inside.

Pischei Teshuvah (8): Tif'eres l'Moshe is lenient if the Seforim do not touch the top of the box. Teshuvah me'Ahavah (1:9) says that our printed Seforim are Kodesh like Kesivah Tamah.

Rema (ibid.): One may not put them even on the steps in front of the Aron Kodesh.

Gra (18): Even R. Yochanan forbids putting it on the floor. Steps are no better, for people walk on them.

Pischei Teshuvah (7, citing Tif'eres l'Moshe): If many Seforim fell on the ground at once, and there will be more delay and toil to pick up each by itself than to make a pile and pick it up, one should do the latter. This is like we say in Eruvin (97a), that if one found bundles of Tefilin, and if he brings them one pair at a time he will not finish before dark, he waits there until dark and brings them. However, perhaps Shabbos is different.

Rema (ibid.): One may not put a Sefer Torah on his knees and put his elbows on it. It seems that the same applies to other Seforim.

Source: Beis Yosef (DH v'Chosav citing Hagahos Maimoniyos, citing Maseches Sofrim 3:11).