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Currently, I am using Window 2003 standard with 4GB memory and 14 application Pools in the server.
There are 200+ applications. I am currently rearrange the applications vs application pools and would like to find out
best practice in order to best distributed applications among each application Pools ?

Well this can vary.  In IIS 6.0 I believe you can have 1,000 apps but only 200 will run concurrently.

You can reduce the amount of app pools that are running when in standby (the ones not handling requests but that are using system resources), make the "IdleTimeout metabase" value for the application pool lower.  To do this within IIS manager, make the pool’s "Shutdown worker processes after being idle for" setting on the Performance tab of the application pool’s Properties lower.  Out of the box is 20 minutes, but you can modify this based on what you need it to do.

Keep in mind that this is dependent on many things like what is being served, what's running concurrently, identities of the application pools (network service for example), etc.  Another thing is that if you have a lot of worker processes running within the same app pool, you can start losing resources.

I have this Technet article that may help:
http://technet.microsoft.com/en-us/library/ff426423(v=ws.10).aspx

Also, be mindful that 2003 is coming to end of life in July of 2015 and with 32 bit standard, you are stuck at 4 GB.  Upgrading (if allowed by the business) is something I would recommend in the near future so you can dedicate proper resources to the vast amount of apps you are hosting.  This gives you a little less than a year to prepare and upgrade .NET apps if that's what you are running.

I hope this gives you a good starting point.

-Esteban