Funnily enough I have not found many people complaining about the lack of proper email integration with discussion boards. Probably because they are all using Outlook 2007 by now :-) and there you have full Discussion Board integration just like you can integrate tasks, contacts and calendars.
Within Sharepoint there is the option to accept incoming emails for lists and libraries. This feature works like a dream. First you configure your incoming email settings in Central Administration (Operations Tab) and then configure an incoming email address for the list or library in its settings (Communications column beneath RSS settings).
So far so good. Now you should be able to start new discussions simply by sending an email to a discussion board. An example email address could look like email@example.com . Cool! But how do you reply to a thread?
This is where the main option is missing. You can only reply to a discussion if you subscribed to it and received the discussion in your email. But guess what, that option does not exist in SharePoint.
You might think, "hey, let me try alerts" And although they are a great tool for all other kinds of lists and libraries, they are not meant to be discribution channels for discussions and thus replying to an alert will not get you anywhere near where you want to be. Two problems. first, the sender is a fixed email address for all alerts, so replying to it will not end up in the list that you want to end up in, and secondly the format of the email is totally wrong for email threads.
Now If you posted the original thread via email, opened that email from your sent items, replied to it by including the original text in the email and changed the To: email to the one of the discussion board, it would actually work! Whopee!
So SharePoint is clever enough to strip out the "Re:" bit, match the subject up and also match up the body to figure out which post you're replying to.
Thus the only feature which is really missing is the Discussion Subscription mechanism and the distribution of discussions to the subscribers.
There are a few options thinkable. Now these are just hypothetic...
1) Create an event handler for the discussion board which reads out the alerts set up on the item/list and sends an email to the subscribers.
PRO: simple to set up and maintain
CON: users receive two emails, the subscription and the alert.
2) Create a feature which replaces the alert feature on that discussion board and maintains its own list of subscribers which then get "spammed" through an event handler.
PRO: users only receive on email
CON: need to create additional User Interface components for subscribing and unsubscribing to discussions and discussion boards
3) Create your own custom email alert handler to catch the alerts and reformat them by adding the original body and changing the reply to field to the list's email address. here is a great article to get you started on this route:
How to create a custom email alert hander by Microsoft http://support.microsoft.com/kb/948321
Just the SPUtility.SendEmail function does not allow you to specify a reply to address, so I would use a different email sending function such as the built in smtp functions in System.Net.Mail.
Two great articles on customising alert templates in general:
1) How to customise the built in alert template by Brett Lonsdale at Combined-Knowledge http://www.combined-knowledge.com/Downloads/Modify_Alert_Notifications.pdf
2) customising Alert Templates in WSS 3.0 on the SharePoint Team Blog
I've tried playing with the custom alert handler and got as far as sending out minimal streamlined emails but the date stamp on the email is different and thus the email hander is not clever enough to match them up. thus you would need to write your custom incoming email handler for the discussionboard as well. here is a link to get you started: