A lot of confusion surrounds the motions of the daily prayers, particularly the bowing. I have attempted to elucidate things a bit.

Before we discuss the actual bowings, several introductions are necessary.

Biblical Bowing

In the times of the Bais Hamikdash, bowing came in several forms:
Kida – total prostration. This is very difficult to do; it basically involves falling flat on your face and then moving yourself forward with your thumbs.
Kriah – falling to your knees, often as a preparation for Hishatachvaeh
Hishatachvaeh- knees, palms and forehead on the floor
We do none of these; our bowing is referred to a ‘sicha’ or bending.

Extra Bowing

The Gemara says (Berachos 34) that one who bows in any other blessing in Shemonah Esrei should be stopped. Furthermore, the Gemara tells us that making extra bows in Hallel or in the thanksgiving portion of Grace after meals is considered distasteful.
All the Rishonim ask: The Gemara previously recorded that Rabbi Akiva would begin praying in one corner of the room and due to his excessive prostrations would end up in a different corner of the room. They resolve this in several different ways:
• He bowed in the middle of the blessings, not the beginning or end. (Tosfos, Rosh, Mordechai)
• It refers to his own added blessings after he finished the formal Shemonah Esrei (Re’ah , Ritva, Raavad)
• The prohibition is specifically in blessings of thanksgiving. Hodaah has a dual inflection – thanksgiving and submission. When intended primarily as submission Chazal legislate bowing. It is therefore ‘distasteful’ to bow in other blessings of thanks, for that implies a different understanding in the prayers than intended by Chazal. (Taz, Meiri, Chidushei Anshei Shem).
The practical ramifications of this dispute will come into play shortly.

Shemonah Esrei

The only bowings legislated by the Gemara are the ones in the Amidah. The Gemara (Berachos 34) tells us there are four times one should bow; the beginning and end of Avos and the beginning and end of Hodaah.
Additionally the Yerushalmi writes that one should bow together with the Shaliach Tzibur at Modim. (We’ll get back to that soon).
The bowing the Gemara refers to is just bowing ‘like a reed’ and doesn’t involve the bending of the knees. The source of bowing at the knees when saying Boruch is the Zohar in Parshas Eikev, first quoted as a Halachic obligation by the Magen Avrohom (113:4).
According to all opinions, one should revert back to an upright position before uttering the name of Hashem, both in Modim, and in the other Berachos.
All other bowings were added to the prayer service. We will attempt to go through them.

Zokef Kefufim

The morning blessings were originally intended to be said as the actions to which they refer were performed. The blessing of “He who straightens the bent” was initially instituted to be recited as one straightens up first thing in the morning. Now we say them all at once before beginning davening, and this is no longer applicable.

Kaddish

The Shulchan Aruch (OC 56:4) counts five bows that are to be made during Kaddish. The Vilna Gaon strongly objects to this practice, and writes than there should be no bowing during the Kaddish as this violates the precept to not add bowing.

Borchu

The universal custom is to bow when reciting Borchu, both during the davening and when receiving an Aliyah. The Mogen Giborim questions the source of this minhag (which has been around for a while, it’s recorded by the Kol Bo). The Biur Halacha (113) suggests the verse in Divrei Hayamim (1:29:2) which indicates that all bowed when reciting Borchu. He concludes that Minhag Yisroel Torah, and it should definitely be done.
The Magen Avraham brings a dispute as to whether one should bow when reciting Borchu specifically upon receiving an Aliyah. The Aruch Hashulchan writes that the custom was to not bow. Even the Aruch Hashulchan agrees that one should definitely bow at Borchu during davening.
The Shaarei Teshuva writes (57:1) that one should face east until after one completes “Boruch Hashem Hamevorach Leolam Va’ed” The Aruch Hashulchan is dubious about this, and writes that is not Halachically imperative.

Modim DeRabannan

The Yerushalmi writes that when the Chazzan reaches Modim the congregation should bow with him. There are several approaches:
The Shulchon Aruch says you should bow at the beginning, and adds that some say to bow at the end of Modim DeRabannan as well, and he recommends doing so.
The Rema writes the minhag is to say the whole Modim DeRabannan in a bowed state.
The Bach says not to bow, rather to just bow the head slightly, the Mishna Berura comments that this is not the Minhag.

Oseh Shalom – The End of the Amidah

The Shulchan Aruch writes that one should bow and take three steps back at the end of Shemonah Esrei. He should remain bowed and then, after completing the three steps, while still in a bowed position, turn to the left and say Oseh Shalom Bimromav, turn to the right and say Hu Yaaseh Shalom, Aleinu, and then bow forward and say V’al kol Yisrael Veimru Amen.

Kedusha

Some have a custom to bow when saying “zeh el zeh”. The Minhag Yisrael Torah struggles to find a source for this, ultimately attributing it the Lelover Siddur.
The custom to rise up to one’s toes when reciting “Kadosh Kadosh Kadosh” is brought by the Rema (127). The Shelah adds Boruch and Yimloch as well.

Birkas Kohanim

The Magen Avraham (127:3) quotes the Zohar who writes that the Chazzan should face in specific directions when reciting the Priestly Blessing in the repetition. At Yevarechacha he faces toward the Aron Kodesh, at Yishmerecha his right. At Yaer Hashem he faces the Ark, at Eilecha Veyichunecha he faces his right. (Cf. Siddur Yaavetz). The Minhag Yisrael Torah records a dispute as to whether one should bow slightly as well.