The three solutions you stated each cover very different needs.
Manual parsing (simple text search) is the most flexible and the most adaptable, however, it very quickly becomes a real pain in the ass as the parsing required is more complicated.
Regex are a middle ground, and probably your best bet here. They are powerful, yet flexible as you can yourself add more logic from the code that call the different regex. The main drawback would be speed here.
Lex/Yacc is really only adapted to very complicated, predictable syntaxes and lacks a lot of post compile flexibility. You can't easily change parser in mid parsing, well actually you can but it's just too heavy and you'd be better using regex instead.
I know this is a cliché answer, it all really comes down to what your exact needs are, but from what you said, I would personally probably go with a bag of regex.
As an alternative, as Vaibhav poionted out, if you have several different situations that can arise and that you cna easily detect which one is coming, you could make a plugin system that chooses the right algorithm, and those algorithms could all be very different, one using Lex/Yacc in pointy cases and the other using IndexOf and regex for simpler cases.