I have an issue. I have situation where I need to send around 3000 emails per request using SMTP. However, only 30-40 reaches destination.
Do you have any idea what can be a problem and how to solve it. as server side script I am using PHP.
If your looking to inboxing as many emails as possible and you are not sending spam, and prefer to use your own smtp, check them out.
How the big e-mail service providers (Constant Contact, WhatCounts, etc.) do mass e-mails is to put the "campaign" in a queue and send it at a later time. They have dedicated, high-performance delivery software for looking through the queue for new campaigns to send and then send them out at rates exceeding 50,000 messages per minute. Anything you might do in PHP won't even compare.
If you are trying to send from your local computer, that won't work. DNSRBL lookups will identify your computer as being on a "DUN" (Dial-Up Network) and will block the message. Most PHP scripts also have a timeout of 30 seconds in a web server environment but running via cron a PHP script can run as long as it needs to.
You shouldn't send mass e-mails from your main e-mail server either. That's a nice, fast way to get on global blacklists so that you can't send regular e-mail to common hosts (e.g. Hotmail, GMail, etc). The big e-mail service providers have dedicated staff whose job it is to remove themselves from global blacklists. That's a full time job. You are better off paying for the service (don't forget to set up SPF records correctly if you do go this route).
Warnings and advice aside, to answer the question, use a cron job for your PHP script and put the e-mails to be sent out in a queue.