If I say "This methodology can/could be used in the research in this area, e.g. (the relevant paper)", should I use can?
If no examples is given, should I use could? (to emphasize possibility?)
This seems like a fine line with no objective answer. It depends how ready you are to defend your point of view. If you believe firmly (i.e. have good evidence that the method is valid, even if it hasn't been used yet), you can use can. Else, if you consider that your opinion (that the method is valid) may be contested, and you are not sure that it's defensible, use could.