Incest Subtext: Marc and Megan are awfully close with one another, often seen with one arm or shoulder around the other in screenshots, and Megan is always there to advise Marc on social graces. The subtext is subtle but definitely visible.
Jerk Jock: Averted; Lee does have a couple moments of chauvinism or over-competitiveness but is generally a really nice kid.
Shout Out: Done very subtly in "Operation Grow Up". The episode features a villain that can alter his age at will, becoming a child at some points, an adult at some others, but one of his distinguishing traits is that he has a small scar on his chin at all times. Earlier in the episode, Tony is upset because he's too young to see a movie his older siblings are all going to. It isn't mentioned by name, but the poster the children bring back features a very familiar silhouette. Fans of the franchise need not hear more. Sneaky!
Marc's crush in "Operation Crabby Bob" is named Sheena Weston. Remind you of anyone?
Not to mention that Megan as Gravity Girl in "Operation Fun and Games" can easily remind one of Storm.
Super Mode: Happens to Lee, Marc, and Megan in "Operation Fun and Games"
Super Villain: The villains in this show, while they do still have really stupid Freudian Excuses, they're costumed and have powers or gadgets related to their "Theme", the the old show had some shades of it, but this show has more obvious Super Villain inspiration. Even the villains that do return from the original show have underwent a reworked design more befitting of a Super Villain.
Teen Superspy: Just Lee, technically. He's thirteen; his three siblings are a year younger (or two, in Tony's case).
In the second season he ups it up to fourteen while Marc and Megan become thirteen, thus counting as examples as well.
Transformation Sequence: If the way they put on their spy suits in every episode doesn't count (it's simpler than most examples, but still), then the time that Lee, Megan, and Marc turned into super heroes in "Operation Fun and Games" definitely does.
A Twinkle in the Sky: In "Operation: Twins of Trouble" a WOOHP jet does this as it flies off into the distance.
Unsound Effect: The opening sequence is full of them. It's used periodically within the episodes.
We Want Our Jerk Back: Tami becomes the Clarks' friend in "Twins of Trouble" after they save her life, and she ends up causing them more trouble in helping them than she does antagonizing them. Realizing that they liked Tami better before, they eventually let her "save" them so that the debt is paid and she can go back to being the Alpha Bitch.