Gemara

Beraisa: We may put a Sefer Torah on a Sefer Torah or on Chumashim. We may put Chumashim on Nevi'im or Kesuvim. We may not put Nevi'im or Kesuvim on Chumashim, or Chumashim on a Sefer Torah.

Bava Basra 13b (Beraisa - R. Meir): One may put Torah, Nevi'im and Kesuvim together in one Sefer;

R. Yehudah says, Torah must be by itself, Nevi'im must be by themselves, and Kesuvim must be by themselves;

Chachamim say, each of them must be by itself.

Rosh Hashanah 32a (Mishnah): We begin (each of) Malchuyos, Zichronos and Shofaros) with verses of Torah, and finish with Nevi'im;

R. Yosi says, if one finished with Torah he was Yotzei.

Maseches Sofrim (18:3): On Tish'ah b'Av we say four verses from Yirmeyahu "Ha'Ma'os Mo'asta...", and then Tehilim 78 and Tehilim 137. Even though Divrei Kedushah always precede Divrei Kabalah, here Divrei Kabalah are first.

Rishonim

The Rif, Rambam (Hilchos Sefer Torah 10:5) and Rosh (4:5) bring the Beraisa.

Question: It is permitted to join Torah, Nevi'im and Kesuvim into one parchment (Bava Basra 13b). If so, Nevi'im and Kesuvim will be on top of Torah!

Answer #1 (Ran DH Manichin): In Bava Basra it says that Torah is rolled to the middle, and Nevi'im and Kesuvim from the end. Therefore, Torah will always be on top (it is never rolled 'inside' Nevi'im and Kesuvim).

Answer #2 (Tosfos Bava Basra 13b DH Madbik): When they are all together there is no disgrace even if Nevi'im and Kesuvim are above Torah.

Drishah (YD 282:5): It is no disgrace because part of them (Nevi'im and Kesuvim, i.e. the part on bottom) rests directly on the table. Also, they are a Shomer for Torah.

Ran (ibid.): The Gemara does not distinguish Nevi'im from Kesuvim. This implies that they are equal regarding placing one on another.

Ri mi'Gash (Teshuvah 92): One may not put a Gemara on Kesuvim, and all the more so not on Nevi'im (which have more Kedushah).

Poskim

Shulchan Aruch (YD 282:19): We may put one Sefer Torah on another, or a Chumash on Nevi'im or Kesuvim. We may not put Nevi'im or Kesuvim on Chumashim, or Chumashim on a Sefer Torah.

Rema: We may put Nevi'im on Kesuvim or vice-versa. This is if each is bound by itself, but if they are wrapped together everything is permitted.

Drishah (5): This shows that also regarding our Seforim, which are not rolled, one may put Torah, Nevi'im and Kesuvim together, even though Nevi'im and Kesuvim will be on top of Torah when it is opened (to Nevi'im or Kesuvim). However, this is not a solid proof. Tosfos (ibid.) says that it is not disgraceful when Nevi'im and Kesuvim are rolled on Torah. This is because part them rests directly on the table, or because they are a Shomer for Torah. This does not apply to our Seforim today.

Taz (13): It is forbidden to bring a Sefer in order to put it under another Sefer to raise the latter, for then the bottom Sefer is used like a piece of wood! However, if the bottom Sefer is already there, surely one may place another Sefer on top of it.

Aruch ha'Shulchan (22): Rashi (Megilah 27a DH Chumashim) says that Chumashim are Sifrei Torah with only one Chumash. The Ran says that they were written for Kedushas Sefer Torah. This implies that a Chumash not written for Kedushas Sefer Torah, and all the more so a Chumash on paper or a printed Chumash, is no more Kodesh than Nevi'im and Kesuvim.

Shulchan Aruch (283:1): We may put together Torah, Nevi'im and Kesuvim in one parchment. Its Kedushah is not like a Sefer Torah, rather, like a single Chumash.

Rema: This refers to Chumashim on parchment wrapped around rollers. Our bound Chumashim are like Nevi'im.

Aruch ha'Shulchan (6): Whatever is not written on parchment l'Shem Kedushas Sefer Torah (or Nevi'im or Kesuvim) has the same Kedushah. Even Torah she'Ba'al Peh is equal to Torah shebi'Chsav, and either may be put on top of the other.

Ha'Gaon R. S.Z. Auerbach said that the Aruch ha'Shulchan's opinion was not accepted. He and ha'Gaon R. N. M. Karelitz, Shlita hold that a Sidur has Kedushah like Nevi'im or Kesuvim. Ha'Gaon R. C. Kanievsky, Shlita equates its Kedushah to that of a Gemara. Ha'Gaon R. Y.S. Elyashiv, Shlita agrees, but advises not to put a Sidur on top of Seforim, or vice-versa (Ginzei ha'Kodesh 3:30, p.232).

Shulchan Aruch (OC 315:7): On Shabbos one may stand up two Seforim and rest a third Sefer on top of them.

Rema: It is not forbidden (because of making an Ohel) because he does not need the area underneath.

Mishnah Berurah (30): The Taz forbids even during the week unless he needs to learn from all of them, or if the bottom Seforim were already there. The Magen Avraham and Chayei Adam permit.

Aruch ha'Shulchan (ibid.): One should not put a Sefer in another Sefer for a bookmark, unless he needs to use both Seforim.

Shulchan Aruch (OC 153:2): If one sold coverings (of Seforim), the money may be used to buy Seforim, i.e. individual Chumashim, or Nevi'im or Kesuvim. Money of Seforim may be used to buy a Sefer Torah. Money of a greater Kedushah may not be used to buy a lower Kedushah.

Rebuttal (Magen Avraham 2): This connotes that the Kedushah of Chumashim is the same as that of Nevi'im and Kesuvim. This is wrong. Chumashim have a higher Kedushah, so their money may not be used for Nevi'im and Kesuvim.

Mishnah Berurah (6): The Shulchan Aruch agrees that Chumashim (on parchment with rollers) have more Kedushah than Nevi'im and Kesuvim. Our (printed) Chumashim, even if they contain the entire Torah, have less Kedushah than a single Chumash made like a Sefer Torah.

Magen Avraham (OC 28:4): The Bach says that one should make a narrow Tefilin bag in order that the Tefilin Shel Yad will be on top of the Tefilin Shel Rosh and he will remove it first. This is wrong. Since the Shel Rosh is more Kodesh, it is forbidden to put the Shel Yad on top of it. However, perhaps we are not concerned for this when the Kedushos are similar; one may put Nevi'im on top of Kesuvim or vice-versa, even though the Kedushos are different. The Isur is only when there is a major difference in Kedushah, e.g. Torah and Nevi'im.