SubjectRewrite in 3.0.x
The syntax for enabling Subject rewriting has changed in 3.0.x, it is now a more generic rewrite_header option.
This is documented in the UPGRADE file:
The "rewrite_subject" and "subject_tag" configuration options were deprecated and are now removed. Instead, using "rewrite_header Subject \[your desired setting\]". e.g.
rewrite_header Subject ****SPAM(SCORE)****
Warning: if you are running SA through amavisd or qmail-scanner, those apps do their own message rewriting and SpamAssassin cannot perform these rewrites. Here is the FAQ entry for how to rewrite the subject in qmail-scanner.