Should we adopt a common standard of citing scientific papers or should people decide on their own whether they just add a link or cite the paper like you would cite it in a scientific paper?
A common standard would be nice: however I see no need of enforcing it for now.
Can you spell out (in the question) how you would propose to do cites so we can start adopting it if we like?
I don't think we need formal citations, as long as we have a permanent way of referencing particular sources.
Just about all journals use the Digital Object Identifier (DOI) System. I think it's perfect for here since it provides a permanent URL to specific resources. I think that's what we should use for linking to published papers, but I also don't think it needs to be enforced.
Since this is the web, I tend to prefer links. It's usually impractical for people to dig up articles that can't be linked to. This post is a good example of readable, useful linking. Note I'm not commenting on the quality of the references, just that it is useful when done in this fashion.