When we are supporting teachers to completely redesign a course to be fully online or substantially blended we use a very basic design template which doesn't actually mention moodle at all. We don't want their design to be driven by a specific set of tools. Yes they need to have some understanding about Moodle and also other potential online tools not within the Moodle toolbox. But especially when the teacher is new to this we see it as our job to help them think through how their ideas will translate into an actual course.
So we use a MS Word-based "course design template" that helps a teacher focus on designing an activity-based course. Our template is an adapted version of a design tool that several NZ tertiary institutes are using called OTARA. OTARA was first introduced by Kate Hunt and Maurice Moore at a Conference in 2005 (http://www.efest.org.nz/2005/speakers/bio_moorehunt.html) and it has close links to the activities/resources/supports framework proposed by Oliver and Herrington (http://elrond.scam.ecu.edu.au/oliver/2002/edmedia1.pdf).
We incorporate the course design template within a general project management/style guide toolkit - http://ecampus.nmit.ac.nz/moodle/mod/resource/view.php?id=4346. It is important to emphasise that this design plan needs to be completed before any online development occurs. When using a team-based approach or out-sourced development we use version control to debate and adapt the design until it is approved and then the resources and online environment are created. The design plan can continue to be adapted and used as an ongoing summary of how the course is intended to work.
It is early days for us in terms of this kind of rigour for course development so we will no doubt be continuing to adapt the design tools a we go.
There is a new New Zealand-based learning design community called LDNet that is just getting started but includes more discussion and links to alternate learning design models - http://akoaotearoa.ac.nz/communities/ldnet.