I am getting glimpse that my server is being down every now and then, am using beyondhosting VPS. Can anyone suggest me what can I do to be full proof and decide whether its really my server or something else?
There are ping services that SMS or Email you when they get no response.
http://www.poweradmin.com/
Check that one out.
https://www.pingdom.com/#freemodal
Other services for server monitoring include CopperEgg (which I like) and NewRelic. These can give you more detailed alerts, e.g. downtime, cpu usage > threshold, memory usage, response time > some value, etc so that you can get alerted when your server is performing poorly or approaching a bad situation.
The simplest, free solution I would recommend is using Pingdom to monitor your tracking domain and send you an SMS/android/email alert when you incur downtime.
+1 for Pingdom
Here's my downtime for this month from Beyondhosting.
We use pingdom as well.
+1 for new relic....its not cheap but its by far the best.....give you data on everything going on....including mysql...
If you have a basic affiliate site with minimal PHP processing/DB interaction, then 100% go for Pingdom. They have a sweet iPhone app and can even text you when your server is down (you have to buy SMS credits first, of course).
New Relic is a whole different ball game, but holy shit is it awesome. It gives you a breakdown of you application's latency and performance based on the specific queries and PHP classes that run. I was able to get the load time to halve (from ~800ms to ~400ms) on two of my main public-facing pages of a company I run within literally 15 minutes of installing New Relic by weeding out problem queries and optimizing their indexes.
You also get a free t-shirt too... but it's a shirt you'd rarely want to wear in public, lol:

Something different:
http://downforeveryoneorjustme.com
And in case that site seems to be having problems, there's:
http://isdownforeveryoneorjustmedown...eorjustme.com/

Here's a tutorial I wrote a few weeks ago showing you step-by-step how to set up Pingdom monitoring.
NewRelic is indeed awesome, but a lot more complex. Unless what you're doing is pretty advanced, Pingdom's a good starting point.