The SMTP protocol is weak, very weak, but it offers optional headers that are very commonly used. A reply missing those headers either come from a broken email software or is a fake reply:

in-reply-to (rfc 822, 4.6.2):

The contents of this field identify previous correspon- dence which this message answers. Note that if message iden- tifiers are used in this field, they must use the msg-id specification format.

references rfc822, 4.6.3):

The contents of this field identify other correspondence which this message references. Note that if message identif- iers are used, they must use the msg-id specification format.

Spamassassin provides a way to detect missing headers and to match patterns in other headers. To detect a fake reply,testing the presence of the In-Reply-To and References headers in messages with a subject starting with "Re:" is enough.

Here is how it will looks like in your local.cf file:

# define a few primitive first:
# one for subjects starting with "Re:"
header    __SUBJECT_RE     Subject =~ /^Re: /

# one for missing In-Reply-To headers
header   __MISSING_REPLY  In-Reply-To =~ /^UNSET$/ [if-unset: UNSET]

# one for missing References headers
header    __MISSING_REF    References =~ /^UNSET$/ [if-unset: UNSET]

# let's use the primitives to define our filter:
meta   UN_FAKE_REPLY   __SUBJECT_RE && (__MISSING_REPLY || __MISSING_REF)

# end of the filter (description and score)
describe   UN_FAKE_REPLY   fake reply
score      UN_FAKE�_REPLY  2

Updates: Looks like yahoogroups replies are caught by this filter.. thanks yahoo for not using the proper headers.