Hello,
I wanted to open this topic because I discussed about it a lot quite recently and I would like to gather opinions about a specific example involving CCK and taxonomy. This discussion may be useful to Drupal newcomers as reference.
Among those two solutions, what would you do:
1) work with the "story" content type and create a "Content" vocabulary that contains 2 terms "Announcement" and "Blog" that gonna by used to categorize the content type.
2) clone "Story" to "Announcement" and "Blog" content types: you now have two content types that use the same fields.
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Solution 1) brings you taxonomy based browsing: taxonomy urls can combine terms, ubrowser module can ease browsing (or taxonomy_browser when it's updated), etc. Also, as mentioned in a Lullabot podcast, taxonomy is somehow optimized because it stores information by ids compared to CCK. However, if for some reason you want to add fields to your "Announcement" nodes but not to "Blog" nodes, you're a bit stuck because you gonna break your workflow.
With solution 2), views can help you combining nodes. You can add fields whenever you want. Also, you are free to use different permissions for each type of nodes. If your "Annoucement" and "Blog" content types use the same fields forever (title and body), then it does not matter you don't lose anything.