A sefer should be handed from one person to the other; it may not be thrown or tossed around. (Shulchan Aruch Y.D. 282:5)
When taking a Sefer and any item of Kedusha one is to take it with his right hand. (Pri Megadim A.A 206:6) A lefty should use his left hand. (Beer Moshe 2:3:18)
A sefer should not be placed face down (meaning with the sefer open facing the ground). If it is found in this position it must be turned face up. (Rama Y.D. 282:%)
Similarly, a sefer should not be stood upside down (so that the letters on the spine are upside down). If it is found in this position, it must be stood right side up. (Aruch Hashulchan 282:11)
It is prohibited to place anything, except Chidushei Torah, inside a sefer or on top of a sefer (Pischei Teshuva Y.D. 282:17 and Igros Moshe 4:72)
Rav Moshe permits placing blank paper intended for chiddushei Torah in a sefer. (Igros Moshe ibid.) However, the sefer Torah Leshma (306, supposedly written by the Ben Ish Chai) forbids placing blank paper in the sefer since there is a chance that one will forget and not use the paper for his chiddushei Torah.
Many people have a custom of placing their beard hair, that came out while learning, into a sefer. The Sefer Torah Leshma (306, supposedly authored by the Ben Ish Chai) writes that this practice is not allowed since one may not place anything in seforim. A similar ruling was expressed by the Yalkut Yosef (Kitzur Shulchan Aruch 153:17) However, it is reported (Sefer Zecher Tzadik Levracha page 34 and Kerem Shlomo 1:5) that the Zohar owned by the Baal Shem Tov contained his hair and, clearly, if it would be forbidden he would have removed it. In addition, the Sefer Likutei Maharich reports that this seems to be a custom by many and surely there is a kabbalistic reason for it. For practical halacha, a rav should be consulted.
It is proper to kiss one’s sefer before and after using it and it is also a segulah to have good memory.(Kaf Hachaim 155:12, Ohr Tzadikim 22:17, Shemiras Haguf V’Hanefesh page 774)
It is prohibited to use a sefer as a bookmark by placing it inside another sefer. (Pischei Teshuva Y.D. 282:17)
The poskim discuss whether one may fold a page-corner of a sefer so that it serves as a bookmark. Harav Shlomo Zalman Auerbach zt”l permits it (Teshuva printed in Avnei Yashfei vol. 1 203). This is also the view of Harav Shach zt”l and Harav Elyashiv zt”l (Ginzei Hakodesh 3:8). Harav Binyamin Zilber zt”l (Beis Baruch 31:186) questions this. He does recommend that the page should be folded on the margin; not on the spot where there are words printed.
The Gemara rules that one may place Chumashim on top of Neviim (works of the prophets) or Kesuvim (other Biblical works), but that Neviim or Kesuvim should not be placed on top of Chumashim (Megillah 27a; Shulchan Aruch, Yoreh Deah 282:19) One may also not place a Gemara on top of Neviim or Kesuvim. (Beis Lechem Yehuda Y.D. 283)
The Aruch Hashulchan (293:6) maintains that this halachah pertains only to chumashim and neviim which are on a scroll, not to printed and bound chumashim and nach’im. All printed seforim may be placed on each other without a specific order. For practical halacha, a rav should be consulted.