I am trying to implement a web server on to a micro controller as a self learning project.I am considering Atmega16 and Atmega88 as primary options.Need to know which will be the best choice.
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Perhaps obviously the one with the greatest memory resources. Neither part in your short-list supports Ethernet so neither is particularly suited to network applications; you would need an external Ethernet solution - the controller on that is likley to be more powerful and more expensive than the ATMega16/88 in any case.
You could of course use the UART and PPP or SLIP, but that is rather restrictive.

Clifford
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