Markdown syntax for a link is pretty simple:
[Example](http://example.com/)
produces:
Example
But what if the link itself contains a closing bracket?
[Syntax](http://en.wikipedia.org/wiki/Syntax_(programming_languages))
produces:
Syntax)
which is obviously broken.
Edit
Putting the url in quotes does not work
You can try to escape the character:
[Syntax](http://en.wikipedia.org/wiki/Syntax_\(programming_languages\))
Sometimes you need to encode ) with %29.
[Syntax](http://en.wikipedia.org/wiki/Syntax_(programming_languages%29)
E.g.: This was the only method I could find to get a correct Markdown preview in the Atom Editor.
You don't have to scape it at all.
On GitHub, I've just done the following without any problems:
[Slowloris](https://en.wikipedia.org/wiki/Slowloris_(computer_security))
Actually, even here you can use it directly, as you can see here.