The whois database is provided by the registrars. The limit is to help control the server load. You would need to go to each provider of whois DB server and purchase rights to use if you want more. The whois command comes with Linux if it is installed, you can have your script exec the command and return the results.

you must pay for good "Whois Script"

All whois Registrars will have a limit on the data you can retrieve from their Server.
Either go for a paid option (or) use proxies to query their System.

Here are some paid API's pricing:
robowhois[dot]com/pricing
whoisxmlapi[dot]com/hosted_pricing.php

A good and working whois script without limit and without fees on x requests takes time and effort to write, there's a good reason that it doesn't exist any good free script out there.

I have code written for this on the .NET platform but I will not give it away for free of course.

If you really want a flexible Whois script without any limits it may also require a little maintenance if things change.

Last time I did this, I called out into shell (whois) routine and provided a custom whois server, so I can run queries without getting banned.

I captured (and parsed) the output of the shell command.

The only gotcha is .org domains, whois servers for those are hard to come by, I think I only found one.

Checkout the whois script, best and affordable
mkj.co.in/?p=52