The title sequence has been changed to bear some reference to the over 50 disguises that Sydney has worn in the show thus far. Jennifer Garner was not a fan of it.
In the first episode of the fourth season, when Sydney and Vaughn are preparing at the train, Vaughn said "Good Boobs" in Russian at 27:53. In Russian, it sounds like "horoshiye siski". It's specifically the word "boobs", not the word "breasts". And Jennifer responded like it was improvisation, and she knew what it means but didn't expect that.
Alias (2001) Season 4 aired in a new timeslot, moved from Sunday evening to Wednesday evening. The producers saw this as an opportunity to lure in some viewers so decided to eshew the usual cliffhanger style of the show and devote the season to more standalone episodes.
The episode begins with the Etta James classic "At Last" - an amusing reference for fans who had had to wait longer than usual in between Seasons 3 and 4.
From this episode on, Mía Maestro is credited in the opening title sequence, while David Anders and Melissa George are not.