The most commonly confused fraternities at my school are:
Phi Sigma Kappa
Phi Kappa Sigma
Phi Kappa Theta
Kappa Sigma
(We also have Sigma Kappa - though it's hard to confuse a sorority with a fraternity
)
Sigma Alpha Epsilon
Sigma Phi Epsilon
(I think SAE has closed, though.)
Sigma Chi
Sigma Nu
Theta Chi
Theta Xi
Theta Delta Chi
(whew... I think I've just named half the fraternities at my school
)