Hi Stuart,
Some extremely useful suggestions already. Here are my three pennies' worth...
[1]
To teachers - Great questions lead to great online discussions - your thread's definitely proved that point

[2]
To users unfamiliar with forums - use the 'reply' link next to the message you're actually replying to. This allows threaded discussions to evolve. (or the course creator might instead consider setting up multiple 'single question' forums)
Also, if you're subscribed to a forum and are receiving notifications by email, remember not to use the reply function in your email software - this will not reply to the whole group; just to the individual.
[3]
To developers - there's no right or wrong way to use Moodle; it's there to do what you need it to do. Some swear by the inbuilt
activities like the 'Book' and choose to upload all of their resources to each course folder. Personally I prefer to link to multimedia assets that reside on a separate server.
This allows me to point to the same activities from multiple courses and makes updates much easier to roll out.
- but there's an added bonus; your resources can then run off a php backend and be designed as complex web applications that 'plug-in' to the VLE by using Moodle variables passed as parameters in the URL that opens your resource.
For example: add resource > 'link to a file or website'. Use the Parameters options at the bottom of the page to pass a user's Moodle id to your web application:
http://mysite.ac.uk/patient-record-system-simulation/index.php?id=234