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Setting up and customizing mail server to store mails in desired way

I'm creating a website(say somesite.com) in Java. A part of the website is: users are provided with e-mail address (username#somesite.com)
and can send & receive emails using the e-mail address and the website.
Now, the problem is to setup a mail server. I tried hMailServer but hMailServer uses its own database tables which is very difficult to
use with the website database design.
Is there anyway to use mail server but store those emails in the way I want
(in website database tables)?

I don't know if this reach your expectation, but take a look at Apache James:
http://james.apache.org/server/index.html

Thunderbird api to send a mail via Java

I have been using Java mail API to send mails generated through the Java program. What I want to do now is to send a mail through Thunderbird mail client so that the mail get saved to the sent items folder of the user and the user can resend a mail if it has failed.
I also would like to know if it's possible to get a delivery report in the Java mail API.
Edit
I found out that our mail server is POP3 and it doesn't store mail. So is it a good idea to send another mail to the sender as well and define a rule that categorize those messages?

even if you send it with the java mail api (well gmail at least), you will still be able to see in the sent folder using thunderbird. as a matter of fact, 5 minutes ago, I saw this using a website that I build. I am sending emails using Java API, and when I check the send folder I can see them.

The InBox / Outbox in Thunderbird are normally mapped ti your IMAP-Account. The IMAP-Account is set on a mail server. All your mails and folders are stored on that mail server. the client (Thunderbird) only shows the contant from the server. By remote calls (IMAP-protocol) you can create/delete/edit/move folders and mails on the server. Sending a mail is not part of IMAP. Here you use the SMTP-Protocol. When you configure a mailaccount in Thunderbird you must configure IMAP & SMTP. When you send a mail Thunderbird does the following steps:
- Send Mail by SMTP-Protocol
- Create Mail in Outbox by IMAP-Protocol
SMTP & IMAP are totally different. But if you want to send a mail and see this mail in your outbox you must use both. You can program the same workflow with the java mail api.

If I get your question right, you are looking for a way to trigger mail sending via Mozilla Thunderbird from a Java program (an external program / software running on the same local machine).
You can achieve that via different methods:
calling the Thunderbird binary with command-line arguments
via SimpleMAPI, which Thunderbird supports
via XPCOM, also built into Thunderbird
What you won't be able to achieve easily is getting feedback from Thunderbird about the outcome of triggering / prompting the user to send a mail. But you could achieve that by using more difficult ways of integrating Thunderbird with your external software:
read and parse the actual MBOX inbox / mail sent / profile files in a user's profile. "using the X-Mozilla-Status headers (you could) figure out if a message is a new message (etc). A mbox file is essentially just a flat text file that has a seperator between the messages" (parentheses by me, source)
Write a bridging WebExtension Thunderbird Add-On that integrates in some way with your software. An extension has, via Thunderbird's WebExtensions API, essentially a hook for every feature Thunderbird has and your code Add-On could expose these internals in some way to your software.
AFAIK and sadly Thunderbird, as it ships, exposes no API or similar interface out of the box.

Java GroupWise Mail Client

Is anyone aware of a way to retrieve and send mails by talking directly to the GroupWise server.
I want to be able to retrieve mail using Java if possible.
I wrote a Outlook Plug-In that retrieved mail out of GroupWise via the Groupwise Outloop Plug-in (If that makes sense).
Then dropped the message in a directory where I retrieved it with a Java App.
The problem is that I cannot add more than one GroupWise account in Outlook and need to.
I had a look at this question, but would like to know if there is a Java API
that will allow me to retrieve/send mail from the GroupWise server in a JavaMail like manner.
Thanks.

GroupWise allows mails to be retrieved using IMAP and POP3 which are standard supported by JavaMail. (And outlook too for that matter)
Sending mail should also be possible using smtp.
If it is for plain email I prefer to use these basic proptocols like smtp, pop3 and imap because they work almost everywhere, anytime and on any platform. They are less feature rich than the proprietary protocols, but that point is often not very relevant since many of these features are only meaningful for a subset of the mailclients out there.

Implementing an email server in java

What all language components will have to be used for implementing an email service system using java?

If you want to implement an email server (SMTP, IMAP, POP3) - there is already Apache JAMES. It's open-source, so you can look into its sources if you insist on making one.
If you want to just send emails, having an already installed SMTP server, then use Simple Java Mail or commons-email. Both sit on top of Jakarta Mail (previously JavaMail) and are very developer-friendly.

for SMTP subethasmtp rocks

Maybe look at Apache JAMES.
The Apache JAMES Project delivers a rich set of open source modules and libraries, written in Java, related to internet mail and news which build into an advanced enterprise mail server.

Possible to connect to Outlook WebMail via Java?

I want to create a java program to connect to an outlook webmail server to check for unread emails. I am not looking for an open source java based email client etc.. etc..
I am basically asking if it is possible to create a Java interface to an Outlook Webmail Server. I have been trying to hunt down how I would even begin to do this and it isn't inherently clear. Thanks..

You can use WebDav interface before exchange 2007 or EWS (Exchange Web Services)in Exchange 2007+
EWS Reference - http://msdn.microsoft.com/en-us/library/bb204119.aspx
Also a blog that may start u off with webdav
http://blogs.msdn.com/dotnetinterop/archive/2008/07/21/connecting-java-to-exchange-over-webdav-with-apache-httpclient.aspx

You could also try to have a look at the free exchange clients. Maybe you'll find informations regarding the protocol there.

Apache is developing a API for it Apache POI using which u easily can connect to outlook....