Why did HaSh-m find it necessary to instruct Yitzchak not to be afraid? What might he have been afraid of?
Seforno: HaSh-m was actually reassuring him that his estate would not diminish on account of the Pelishtim's quarrels, since on the contrary, He would bless him with even more wealth. 1
Ramban: Now that Avimelech expelled him from Gerar, and the Pelishti shepherds had quarreled with him over the wells, he was afraid that they would come to kill him.
Ohr ha'Chayim: Since Melech Pelishtim expelled him, he feared that HaSh-m had abandoned him.
Malbim: He feared to publicize Emunah of HaSh-m in public.
Ha'amek Davar (to 26:23): He was afraid to enter Be'er Sheva, lest also the nobles there envy him.
Indeed, the Rashbam attributes Yitzchak's moving to Be'er Sheva to the fact that he was afraid of the Pelishtim - though he gives no indication as to whether he was afraid of them harming him monetarily (like the Seforno) or bodily (like the Ramban).
How did HaSh-m qualm Yitzchak's fear?
Ramban: By putting it into Avimelech's mind to pay him a visit together with Pichol his commander-in-chief and a group of friends. In so doing, he displayed a higher degree of honor than he did to his father Avraham.
Ohr ha'Chayim: HaSh-m said, 'I will not abandon you.'
Malbim: HaSh-m told him not to fear (for Hashgachas HaSh-m will rebuke kings for him, and Avraham's merit will help him).
Ha'amek Davar: He said, 'I will be with you; they will not expel you from here.'
Why is the Berachah in the merit of Avraham, and not in Yitzchak's merit?
Moshav Zekenim: If a Tzadik constantly engages in Torah, and commands his son to do so, after he dies, HaSh-m attributes the son's merits to his father. 1
Seforno: Refer to 26:5:2:1.
Oznayim la'Torah: Chizkiyahu ha'Melech was extremely upset when HaSh-m assured him that He would save Yerushalayim from the army of Sancheriv on the merit of his ancestor David - because salvation on the merit of somebody else is degrading. There is nothing wrong with being blessed on the merit of one's ancestors.
What is meant by "E-lokei Avraham"? (HaSh-m is G-d of the entire world!)
Ha'amek Davar: I gave special protection to him. This is like the blessing we recite, 'Magen Avraham.'
What increase is HaSh-m blessing Yitzchak with? Avraham's Berachah to have many descendents already applies to Yitzchak, and he himself was blessed with prosperity!
Ha'amek Davar #1: He will have many descendents who engage in Torah. This is "ba'Avur (for the benefit of) Avraham Avdi."
Ha'amek Davar #2: Your seed will be great in the eyes of the nations. This Berachah was said at night, a sign of exile - even in exile, Yisrael will be great in the eyes of the nations, due to learning Torah diligently.