Anvilicious: As the show began to focus more and more on terrorism (particularly Muslim extremism), it dropped an awful lot of anvils about how racial profiling just makes sense and how liberals are putting the American people in danger by making it harder for the FBI to do their jobs. The show was one of the first dramas conceived and produced post-9/11, and the level of pro-government jingoism would probably be considered in bad taste today.
Harsher in Hindsight: In "Hit and Run," Sue is held hostage and blindfolded so she won't know where they're going. She panics, saying, "I'm deaf! My eyes are everything to me!" A scary moment for the character, made harsher by the knowledge that the real Sue Thomas started gradually losing her sight later in life, and that could happen to the fictional Sue Thomas as well.
Ho Yay Shipping: Although there isn't much slash in the fandom, there are a few Bobby/Jack fanfics. Shipping Goggles help the pairing come out in a few episodes, notably "The Gambler."
Mary Sue: Sue. Completely flawless and loved by all.