Some members have the abilkity to flag posts and after a certain number of flags they disappear. Otherwise there would be a lot more spam. Occasionally people do the same thing to a comment or story they find objectionable for some reason.
Articles killed by user flags will have either "[flagged][dead]" or "[dupe][dead]". Comments killed by user flags will also have the "[flagged]" designation.
Articles that have only "[dead]" were killed either by a moderator, or by the site's software (e.g., due to the user or the domain being banned).
An article can be marked as "[flagged]" but not "[dead]" if it was killed by user flags and later revived by users (using the "vouch" function).
Dead articles won't be displayed unless you're a logged-in user who has "showdead" enabled in your profile.