Since my question is getting longer and longer, I decide to re-write the whole question to make it better and shorter.
I run my website on dedicated server with 8GB
I had a similar problem with PHP:
1) Check your error logs. Eliminate EVERY error before continuing. 2) Consider modifying your apache configuration to eliminate unused modules - this will reduce the footprint needed by PHP - here's a great link for this - it's specific to Wordpress but should still be very useful http://thethemefoundry.com/blog/optimize-apache-wordpress/
To give you an idea of the kind of bug I found, I had some code that was trying to post content to Facebook, Facebook then modified their API so this broke, I also used a 'content expirator' which basically meant that it kept retrying to post this content to Facebook and leaving loads of objects lying in memory.