I find that Mail::Audit and Mail::SpamAssassin work well together. Here is my filter code (for a kmail client):

#!/usr/bin/perl
#
# A cutsom filter to process my email
use Mail::Audit;

open LOG, ">>/home/kvale/.audit_log";
print LOG localtime() . ": ";

my $item = Mail::Audit->new( nomime => 1 );
my $subject = $item->subject();

if ($item->subject =~ /\[SPAM\s+\?\]/i) {
   print LOG "phy spam: $subject\n";
   $item->print_out();
}

use Mail::SpamAssassin;

my $mail = Mail::SpamAssassin->new();
my $status = $mail->check( $item );

if ($status->is_spam()) {
   $item->replace_header( subject => '***SPAM***' . $subject);
   my @report = split /\n/, $status->get_report();
   shift @report until $report[0] =~ /^Content analysis/;
   print LOG "SA Spam: $subject\n", join "\n", @report, "\n";
   $item->print_out();
}

print LOG "OK: $subject\n";
$item->print_out();
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Note that M::SA methods work nicely with M::A objects.

It is not true that new tests cannot be written into SpamAssassin. Look in the rules directory for info, write some yourself, and put them in your .cf file. If your rules need more than the builtin methods can offer, it is pretty simple add your own module with the custom code. If you don't want to do that much hacking, SA 3.0.0 will have a plugin framework for these sorts of expansion needs.