Pulling emails into my .Net Application

I’m looking for a “best practice” or guidline on this one. My .Net application needs to pull specific emails from Lotus Notes and add their text and attachments into my application’s database. I’ve seen various samples on doing this type of thing, but what is the best practice based on other’s experience?

Should I integrate my code into the notes client to push data to my app, or should I use com interop to reach out to the domino server from my app to get emails?

This is a legal case management system that needs to associate case related emails to the cases in my system.

Thanks for any suggestions!

-Glenn