I know that in first look many users mark this question as duplicate, but after reading more than 10 question I did not get any satisfactory answer, almost all question has
I know this already has an accepted answer but this is for others who might have had the same problem like me and ended up here. I had a website and mails send from my website ended up in spam boxes. Even if I tried using phpmailer and adding our companies mail-server as an SMTP.
However this could easily be resolved by sort of white listing the IP address of the website to the send filter of your mail server. How this is done exactly I don't know because the admin of the mail server did this for me(google it I guess).
Doing this means that if the receiving side does a DNS lookup or an IP lookup to your mail server. The mail-server tells the receiving side that it indeed was sent from him or his associating IP addresses and therefor it will not end up in the spambox.
However if you do this there is no need for the phpmailer and the standard mail() function works too.
Is there any exact solution on this issue
Unfortunately not. It is a non-trivial issue with much complexity which prevents exact solutions.
Instead you need to find out for each email that is marked as spam what led to the spam scoring of it and reverse-engineer that then to the part(s) of the software and systems you use - either configuration (improve the configuration and setup) or processing (patch the software you use and re-compile/deploy).
If you want to improve the situation here on this website - you wrote that many existing questions are disappointing - please keep a worklog of that doing and document each case. Put this as an answer here so that future users can benefit from that. That would be not doing the same mistakes as the previous users have been done on site not doing this documentation and hence the information is missing.
The accepted answer has a lot of good advice in it. Additionally, adding an SPF record to my DNS helped avoid spam filters. Learn more about SPF records:
http://en.wikipedia.org/wiki/Sender_Policy_Framework
Microsoft has a tool to help create such records:
http://www.microsoft.com/mscorp/safety/content/technologies/senderid/wizard/