Basecamp lets you link to messages, comments on messages, to-do items, etc. It has a robust per-project auth/permissions system. Other collaboration sites offer

Basecamp lets you link to messages, comments on messages, to-do items, etc. It has a robust per-project auth/permissions system. Other collaboration sites offer something similar. In general, when dealing with work that occurs via emails, it seems like it's easier to build a separate system that has email notifications, versus trying to glue features onto email.