Why does the Torah see fit to insert the first phrase in the Pasuk, "All these are the tribes of Yisrael..."?
Targum Yonasan: To tell us that they were all Tzadikim. 1
Malbim: Each of the 12 is 'contained' in all 12, just like the power of a particular branch in a tree in contained in the tree.
Even Reuven, Shimon and Levi, whom Yaakov had rebuked.
How can the Torah write that Yaakov blessed the 12 tribes, seeing as he rebuked Reuven, Shimon and Levi (and did not bless them)?
Rashi: The additional phrase "and he blessed them" teaches us that all twelve sons (including Reuven, Shimon and Levi) were included in the blessing. 1
Seforno, Ha'amek Davar: "And he blessed them" means that he gave them all a Berachah over and above the Berachos listed above.
Ohr ha'Chayim: Yaakov's harsh words were their Berachah. In his rebuke of Reuven, he called him Bechori; Chazal learned from this, that the Bechorah will return to the Bechoros. 2 Tzadikim see to the future. Yaakov strove to acquire the Bechorah from Esav, lest Esav have a share in the Avodah in the future. Even though the Avodah was given to Levi, [had Esav not sold it], they would be equal, and both would serve in the end, for we ascend in Kedushah and do not descend. Also Shimon and Levi, it was a Berachah to curse their overpowering [anger] that ruins. Also scattering them was for the sake of attaining happiness.
Malbim: It was necessary to bless 12. The great world has 12 boundaries and diagonals, 12 Mazalos (constellations), 12 ways to order the letters of Shem Havayah, and 12 gates of the firmament. Each Shevet draws its Berachah from the Yam, 3 which stood on 12 [copper] oxen. There are always 12 Shevatim. Efrayim and Menasheh (i.e. Yosef) count as two only when Levi is not counted. When Levi is counted, e.g. on the Urim v'Tumim and on Har Gerizim, Yosef counts only as one. Moshe set up 12 Matzevos corresponding to the Shevatim, Yehoshua took 12 rocks from the Yarden, and Eliyahu built a Mizbe'ach (on Har ha'Karmel) from 12 rocks.
Birkas Shimon: I did not find this Chazal. Some cite Sifrei Beha'alosecha, but that does not discuss Avodah!
Shel Shlomo, in which Kohanim would immerse (Melachim I 7:25).
What is the significance of the phrase, "v'Zos Asher Diber Lahem Avihem"?
Hadar Zekenim, Rosh, Ba'al ha'Turim: Yaakov ended his Berachah with the word v'Zos, and that is the word with which Moshe began blessing Bnei Yisrael (v'Zos ha'Berachah). 1
Ha'amek Davar: "Diber" implies harsh speech, i.e. to Reuven, Shimon and Levi. "Va'Yevarech Osam" teaches that he also blessed them, even though the Berachah is not written in the Torah.
Taking his cue from Yaakov (as David ha'Melech wrote in Tehilim, "mi'Zekenim Esbonan" (Tehilim 119:100)). Hadar Zekenim - Yitzchak concluded his Berachos to Yaakov with "va'Yikra Yitzchak El Yaakov," and Yaakov began with "va'Yikra Yaakov." Moshe ended with "Ashrecha Yisrael," and David began [Tehilim] with "Ashrei ha'Ish."
What does the Torah mean when it writes, "Ish Asher k'Virchaso Berach Osam"?
Rashi and Rashbam: It means that each one received the Berachah that would later apply to him. 1
Seforno: He gave each son the Berachah that suited him personally - Yehudah, concerning Malchus; Yisachar, concerning Torah; and Levi, the Avodah.
Ohr ha'Chayim: It is what is appropriate for him according to his Neshamah and his deeds. There is [one whose attribute is] Kehunah, and there is kingship, and there is the crown of Torah, and there is Gevurah, and there is wealth, and there is success. Via Nevu'ah, Yaakov gave to each what is appropriate for him - the king with kingship, the Kohen with Kehunah... It says "Osam" (plural), for the Berachah to each helps him, and all his brothers. E.g. if the king's hand will be on the back of the neck of his enemies, this benefits all his brothers. Similarly, when you increase the attribute, influence or level of one of them, his brothers also receive something.
Malbim: He blessed each according to his source above. Until now, the heart and Segulah were stored in one person in each generation. He was Mekadesh Shechinas Hashem for all spiritual benefits. From now, the source was divided into branches. First it was divided into 12 Shevatim (branches). With Yaakov, their source, there were 13, the Gematriya of 'Echad.' A Midrash says, his sons said, just like there is in your heart only One, also in our hearts! They were united, just like [the branches] were united in Yaakov, the source. Even though each received his own Berachah, they all share in all the Berachos. The Berachah of each was needed for the Klal.
Ha'amek Davar: Like they will be blessed at the time they inherited the land (e.g. Asher will be blessed with an abundance of oil - PF), so Yaakov blessed them now (via Ru'ach ha'Kodesh) that it will be so.
Rashbam: As Yaakov specifically stated in 49:1.
Why, following "Ish k'Virchaso" (singular) does it write "Berach Osam" (plural), and not 'Berach Oso'?
Rashi: To teach us that, although Yaakov gave Yehudah the strength of a lion, Binyamin, the 'Chatifus' of a wolf and Naftali, the agility of a gazelle, he incorporated each tribe (including Reuven, Shimon and Levi) in the Berachos of each of the other tribes.
The verse implies that Yaakov blessed 12 tribes. Yaakov said that Efrayim and Menasheh will be [two], like Reuven and Shimon. If also Levi is counted, there are 13! If Levi is not counted, for he was rebuked, and not blessed, also Reuven and Shimon should not be counted!
Ohr ha'Chayim #1: Efrayim and Menasheh count as two only after Yetzi'as Mitzrayim. This is a poor answer.
Ohr ha'Chayim #2: Shimon and Levi together are counted as one, for Yaakov addressed them as one.
QUESTIONS ON RASHI
Rashi writes: "'He blessed them' - ... Since he gave the might of the lion to Yehudah [specifically]... I might think that he was not included in all the [other] blessings; thus the verse says, 'blessed them' (in the plural)." If so, all the sons received equivalent blessings!
Gur Aryeh: Yehudah would receive this blessing (the might of a lion) fully; while along with him, each of his brothers would receive some part of it. Yaakov included them all, such that the blessings would overlap in some aspect.
