There is a style sheet attribute in apex:inputcheckbox (http://www.salesforce.com/us/developer/docs/pages/Content/pages_compref_inputCheckbox.htm)which can help you use the attributes(like box-shadow:) from CSS to remove the shadow off the checkbox when shown on VF page: sample shown for s1 platform for checkbox - http://intmist.wordpress.com/2014/02/16/salesforce1-look-and-feel-customise-visualforce-pages-for-salesforce1/
There is a style sheet attribute in apex:inputcheckbox (http://www.salesforce.com/us/developer/docs/pages/Content/pages_compref_inputCheckbox.htm)which can help you use the attributes(like box-shadow:) from CSS to remove the shadow off the checkbox when shown on VF page:
sample shown for s1 platform for checkbox - http://intmist.wordpress.com/2014/02/16/salesforce1-look-and-feel-customise-visualforce-pages-for-salesforce1/