I just started using Movable Type this week, and went through the same search, but didn't find anything that worked the way I wanted. So I ended up writing a plugin to do text formatting using my Text::Multi module. It may not work for you as-is, but it's short enough that it could get you started writing a plugin that does work just the way you want it...

# JasonKohles::TextMulti plugin
# Copyright 2008 Jason Kohles
# <email@jasonkohles.com>
#  http://www.jasonkohles.com/
#
package JasonKohles::TextMulti;
use strict; use warnings;
our $VERSION = '0.1';
our $ID = '$Id$';
use base qw( MT::Plugin );
use Text::Multi;  

MT->add_plugin( __PACKAGE__->new( { 
    id              => 'textmulti',
    name            => 'TextMulti',
    version         => $VERSION,
    author_name     => 'Jason Kohles',
    author_link     => 'http://www.jasonkohles.com/',
    plugin_link     => 'http://code.jasonkohles.com/MTTextMulti/',
    doc_link        => 'docs.html',
    description     => 'Text::Multi Format Filter',
    registry        => {
        text_filters    => {
            text_multi      => {
                label           => 'Text::Multi',
                docs            => 'docs.html',
                code            => sub {
                    my $parser = Text::Multi->new(
                        default_type => 'Markdown'
                    );
                    $parser->process_text( $_[0] );
                    return $parser->render;
                },
            },
        },
    },
} ) );
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