While I'm still not entirely sure exactly what you're doing (some examples would help), I can't help but think that your 'linked_tables' and 'unlinked_tables' would be better off as hashes so that you wouldn't have to iterate through them quite so often:

Anonymous block for scoping
{
    my( %linked_tables, %unlinked_tables);
    
    #------------------------------------------
    sub _get_table_relations
    { 
        my( $self,$tables,$conditions ) = @_;

        #prep lists
        @unlinked_tables{keys %$tables} = undef;
        %linked_tables = ();
        my @tables_nolinks = ();

        #no relations to be found if there's only one table
        {
            no warnings;
            return if scalar( %unlinked_tables ) <= 1;
        }

        # try to find a link for each of the supplied tables
        for my $table ( keys %unlinked_tables )
        {
          next if exists $linked_tables{$table};
          push @tables_nolinks, $table
           unless $self->_table_relation_helper($table,$conditions);
        }

        csWarn(class=>csErrorClass('CODE_PARAMS'),
               severity=>csErrorScale('MODERATE'),
               message=>'Could not find relations '.
                        'certain tables in this view.',
               debug=>"tables without relations:".
                      join(',',@tables_nolinks)
              )
            if scalar( @tables_nolinks );

        return 1;
    }
    #---------------------------------------------
    sub _table_relation_helper
    {
        my ($self,$table,$conditions) = @_;

        foreach my $table2 (keys %linked_tables,
                            keys %unlinked_tables)
        {
            # a link exists
            if( exists $self->{_links}{$table,$table2} )
            {
                #store the conditions of our found relationship with
                #our other conditions
                push @{ $conditions->{axioms} },
                    ( $self->{_links}{$table,$table2}{op}
                      eq $conditions->{op}
                      and ( $conditions->{op} eq 'and' or
                            $conditions->{op} eq 'or' )
                    )
                    ? @{ $self->{_links}{$table,$table2}{axioms} }
                    : { %{ $self->{_links}{$table,$table2} } };

                #first check to see if $table2 needs linking
                if (exists $unlinked_tables{$table2}) {
                  delete $unlinked_tables{$table2};
                  $self->_table_relation_helper($table2,$conditions)
                        unless $table2 =~ /\s/;
                }

                #then add $table to $linked_tables
                $linked_tables{$table} = undef;
                return 1; #short circuit
            }
        }
        return 0;
    }
}
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