We normally check our site SEO specific keyword positions by using the Google Adwords Preview tool by setting geo location as USA and preferred extension as .com .
We also verify the keyword positions using the "Google Global" addon as well..but from last couple of months there is LOTS of difference in keyword positions to both Preview tool , addon and google.com with &gl=us.
For Ex: a 2-word phrase for my site in preview tool shows in 6th / 7th position and where as in google global and google.com shows as 4th position.
We see similar results for related phrases.
What is the best practice to check the SERP report for a website. Please advice us
[edited by: tedster at 4:23 pm (utc) on Aug 6, 2012]
IMHO there is not a best practice for ranking reports. It is more about being aware of the many pitfalls and inaccuracies that exist. Google is trying to personalize as many serps as possible and that can greatly impact your rankings. Ignoring personalization, Google might change your rankings based on time of day. So if you check your rankings at 2 AM, you might see very different rankings from 2 PM.
I tend to monitor keyword rankings more by the traffic levels in analytics. When analytics shows something interesting I then turn to ranking reports to try to better determine what is going on. Of course as more and more keywords become blocked in analytics this method becomes less reliable.