1. Assign users meaningful names on signup. I pull them from the email address (whatever precedes @ if the username isn't already used in the system). This works out much better than assigning names like "user14132" because it makes casual participants seem more involved than they otherwise would.
2. Also, there's a huge difference in site engagement between burying comments after a splash page and putting them on the front page sidebar. There is a trade-off between getting people into your funnel and encouraging casual participation. If you're building community it will come at a cost.
3. Send out email notifications on direct replies in community areas (but be careful not to open your systems to spamming). People love getting automatically notified whenever someone replies to them.