Why, after Yosef removed his sons from Yaakov's knees, did Yosef prostrate himself to his father?
Rashi: He bowed as he retreated backwards from before his father. 1
Ha'amek Davar: Yosef wanted to bow before Yaakov face-to-face (i.e. without an interruption), to thank him for applying "u'Kehal Goyim" (35:11) to Yosef's sons, and not to other grandsons of Yaakov.
Gur Aryeh: He did so specifically then; for that is proper respect when leaving the presence of an important person.
Whose knees were they between (before Yosef removed them)?
Midrash Sechel Tov, Bechor Shor, Seforno: They were between Yaakov's knees.
QUESTIONS ON RASHI
Rashi writes: "After Yaakov had kissed them... [Yosef] steadied them... so [Yaakov]could lean his hands upon them to bless them." But Yaakov had, at first, declared them unfit for a blessing (Rashi to 48:8)! How did Yosef know that Yaakov now agreed to bless them after all?
Gur Aryeh: Rashi emphasizes that Yaakov had kissed the children. 1 That is what indicated to Yosef that Ru'ach ha'Kodesh had returned to Yaakov, enabling him to bless them. 2
Rav Hartman (Mechon Yerushalayim edition of Gur Aryeh): A kiss shows connection. We likewise find that Yitzchak requested a kiss from Yaakov in order to facilitate his blessing (27:27). (When he later acquiesced to bless Esav, there was no kiss.)
At first glance, this comment seems difficult! Yosef knew that Yaakov agreed to bless the children, because he said explicitly, "Please bring them to me, and I shall bless them" (48:9)! Perhaps, at that point, Yaakov only agreed to give his own personal blessing; and Yosef did not yet know if his Ru'ach ha'Kodesh had returned. The kiss is what indicated that indeed it had. (CS)