Has there been a lexer that takes in much more than a regular language?
FORTRAN is famous for having some difficult to lex constructs, but those difficulties result probably more from having been designed before the classification was established (or at least known in programming circles)
Several languages are described with a type-3 lexers but some characteristic are easier to handle by feeding information from the parser to the lexer (C/C++ typedef, C++ templates, Ada/VHDL attributes)
Several languages have layout rules (Python, Haskell) which are usually not described as type-3 lexers (I don't know if it is possible to do so or not)