Off the top of my head I can think of these:
-Lissandra's Q (shatters past first target)
-Sion's E (Through minions)
-Velkoz's Q can travel further if fired at a right angle
-Viktor's E/Rumble's Ultimate can hit outside of it's indicated range
-Urgot's Q gets increased range when homing.
-Nami's W can bounce outside of the range of her indicator (if used on an ally it can bounce to an enemy far away).
-Master Yi's Q can hit enemies outside of range by bouncing through minions.
-Miss Fortune's Q can bounce outside of the initial range (although it does have a separate range indicator for the bounce).
A couple I wasn't sure about:
-Syndra's E's range indicator is accurate (when considering the knock back effect on champions) but the knocked back dark spheres can travel beyond the range indicator)
-LeBlanc's E's tether will break outside of a certain range, but until it has connected with a target it will not break (so you can Distortion in, cast chains, distortion out and the chains will still connect even though it is outside the range it should be).