I'm looking into what it would take to add a feature to my site so this is a pretty naive question. 
I'd like to be able to connect buyers and sellers via an email message once the buyer clicks "buy". 
I can see how I could do this in java script, querying the user database and sending an email with both parties involved. What I'm wondering is if there's a better way I can do this, playing monkey in the middle so they only receive an email from my site, and the it's automatically forwarded to the other party. That way they don't have to remember to hit reply-all, just reply. Also their email addresses remain anonymous. 
Again assuming I generate a unique subject line with the transaction ID I could apply some rules here to just automatically forward the email from one party to the other but is there an API or library which can already do this for you?
What you're describing would be handled largely by your backend.  If this were my project, I would choose the following simple route:
Store the messages the buyers/sellers send in your own database, then simply send notification emails when messages are sent. Have them reply to each other on your own site, like Facebook and eBay do.
An example flow would go like this:

(Gather the user and buyer's email addresses via registration)
Buyer enters a message and clicks 'Send Message' button on seller's page
Form is posted (via AJAX or via POST) to a backend script
Your backend code generates an email message

Sets the 'To' field to the seller

Your seller gets an email alert of the potential buyer which shows the buyer's message
The Seller then logs on to your site (made easy by a URL in the email) to respond
The Seller enters a response message on your site and hits 'Reply'
Buyer gets an email notification with the message body and a link to your site where they can compose a reply.

...and so on.  So, replies would have to be authored on-site, rather than as an email 'reply.'  
If you choose to go this route, there are some simple 3rd party "transactional email" providers, which is the phrase you'd use to find them.  I've personally used SendGrid and found them easy to set up and use.  They have a simple plug in for every major framework.  There is also Mandrill, which is newer but gets good reviews as well.
Email API for connecting in a marketplace?