This is all I've been able to scrounge up after much digging.
SEASON 3
Put in Disc 5, Select the Bonus option at the main menu. Select "The Museum of Television and Radio: Creating Characters" option. Then, press, UP, UP, UP, UP to highlight a hidden Rambaldi symbol in the lower right corner. Press ENTER to view a clip featuring Jennifer Garner.
SEASON 4
>> Put in DISC 6 >> When the Main Menu appears, press the LEFT arrow 2 times (go to Bonus) and press ENTER >> When the Bonus menu appears, press the DOWN arrow 4 times (go to Deleted Scenes) >> When it is highlighted on Deleted Scenes, press the DOWN arrow 2 times, and press the LEFT arrow 1 time >> If/when five red bars appear under the Alias Season 4 logo, press ENTER to watch this hidden clip of the cast celebrating the Holidays, honoring the crew member of the week, and listening to Ron Rifkin singing loud for all to hear! Santa comes, too!
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If you have DVD capabilities on your computer you dont need to go through all that. Just go to the special features screen, point the mouse over the season four logo and it automatically lights up with the 4 red bars. Click on it to enter and you can watch.
SEASON 5
Disc 4 >> in MAIN MENU: go to EPISODES icon, press left 1 time, press down 1 time, press ENTER or PLAY -- Title: "Carl Lumbly's Trailer"
Disc 4 >> in BONUS FEATURES: go to MAIN MENU icon, press up 1 time, press left 1 time, press ENTER or PLAY -- Title: "The Cargo Ship"
Disc 4 >> in BONUS FEATURES: go to THE NEW RECRUIT: ON SET WITH RACHEL NICHOLS icon, press right 2 times, press ENTER or PLAY -- Title: "Balthazar Getty"
Disc 4 >> in BONUS FEATURES: go to THE BLOOPERS OF ALIAS icon, press right 2 times, press ENTER or PLAY -- Title: "Farewell from the Crew of Alias"