user3029: I'm trying to setup a bitcoin service for my users. How do other sites or exchanges keep track of each users unique Bitcoin deposit address? And how does the application alert the admin/user when a deposit is made successfully after 2 confirmations? 
Which applications can do this? I was thinking of using electrum as it didnt require downloading the entire blockchain. What other apps are there that can do something like to manage users btc. 

user42383: Just run bitcoind on your server and then connect via API to it, here is the reference:
https://en.bitcoin.it/wiki/API_reference_(JSON-RPC)
There are also ready (open source) libs in several languages, which you can integrate in your own apps.
Some examples:

https://github.com/Bit-Wasp/bitcoin-php
https://github.com/Bit-Wasp/bitcoin-lib-php
https://pypi.python.org/pypi/python-bitcoinlib

But your question is too broad to give you a more specific answer, since you have to consider, if you want to hold user funds in one wallet and just identify them by different deposit addresses or a separate wallet with it's own keys for every single user.
In general: If you don't know exactly what you are doing, don't store any private keys on the server, especially if you want to hold someone's funds.

3029: <p>I'm trying to setup a bitcoin service for my users. How do other sites or exchanges keep track of each users unique Bitcoin deposit address? And how does the application alert the admin/user when a deposit is made successfully after 2 confirmations? </p>

<p>Which applications can do this? I was thinking of using electrum as it didnt require downloading the entire blockchain. What other apps are there that can do something like to manage users btc. </p>
 42383: <p>Just run bitcoind on your server and then connect via API to it, here is the reference:
<a href="https://en.bitcoin.it/wiki/API_reference_(JSON-RPC)" rel="nofollow noreferrer">https://en.bitcoin.it/wiki/API_reference_(JSON-RPC)</a></p>

<p>There are also ready (open source) libs in several languages, which you can integrate in your own apps.</p>

<p>Some examples:</p>

<ul>
<li><a href="https://github.com/Bit-Wasp/bitcoin-php" rel="nofollow noreferrer">https://github.com/Bit-Wasp/bitcoin-php</a></li>
<li><a href="https://github.com/Bit-Wasp/bitcoin-lib-php" rel="nofollow noreferrer">https://github.com/Bit-Wasp/bitcoin-lib-php</a></li>
<li><a href="https://pypi.python.org/pypi/python-bitcoinlib" rel="nofollow noreferrer">https://pypi.python.org/pypi/python-bitcoinlib</a></li>
</ul>

<p>But your question is too broad to give you a more specific answer, since you have to consider, if you want to hold user funds in one wallet and just identify them by different deposit addresses or a separate wallet with it's own keys for every single user.</p>

<p>In general: If you don't know exactly what you are doing, don't store any private keys on the server, especially if you want to hold someone's funds.</p>
