1. Discount, used by both RDiscount and BlueCloth, supports limited use of classes in inline text via pseudo-protocols in link-style tags. You can also use inline HTML in markdown. I believe that the latter is what most people do.

2. You can do the equivalent of = in Haml filters by enclosing the Ruby in #{}. For example, where sign_up_path is a Ruby helper method:

    :markdown
      [Sign Up](#{sign_up_path})

Personally, in the past I've put large blocks of mostly-static content (eg, a TOS) in a erb template or partial. I now often use the markdown filter for things like help documentation in my sites.