Does Search along with other search engines like google penalize 301 redirects from my naked domain to my regular domain? I want such redirect from to world wide because Google Application Engine doesn't support naked domain names. If at all possible, please provide solutions with up-to-date references. Thanks!

No, you won't be penalised. Google really suggests that you simply set a frequent domain:

Note: Once you have set your chosen domain, you might want to make use of a 301 redirect to redirect traffic out of your non-preferred domain, to ensure that other search engines like google and site visitors know which version you want.

Source: http://world wide owners/bin/