EDIT: A simple possibility to eliminate before getting into more complicated solutions: have you tried setting the character set to utf8 in the text editor in which you're reading the file? This could just be a case of somebody sending you a utf8 file that you're reading in an editor set to say cp1252.
Just taking the two examples, this is a case of utf8 being read through the lens of a single-byte encoding, likely one of iso-8859-1, iso-8859-15, or cp1252. If you can post examples of other problem characters, it should be possible to narrow that down more.
As visual inspection of the characters can be misleading, you'll also need to look at the underlying bytes: the § you see on screen might be either 0xa7 or 0xc2a7, and that will determine the kind of character set conversion you have to do.
Can you assume that all of your data has been distorted in exactly the same way - that it's come from the same source and gone through the same sequence of transformations, so that for example there isn't a single é in your text, it's always ç? If so, the problem can be solved with a sequence of character set conversions. If you can be more specific about the environment you're in and the database you're using, somebody here can probably tell you how to perform the appropriate conversion.
Otherwise, if the problem characters are only occurring in some places in your data, you'll have to take it instance by instance, based on assumptions along the lines of "no author intended to put ç in their text, so whenever you see it, replace by ç". The latter option is more risky, firstly because those assumptions about the intentions of the authors might be wrong, secondly because you'll have to spot every problem character yourself, which might be impossible if there's too much text to visually inspect or if it's written in a language or writing system that's foreign to you.