pop up message from java script

I have a table and it has column as primary defined as checkbox. when  user selects this check box, I have a java script which run some validation and when this validation fails, we want to show a message. I have currently used alert(message) but I do not like the look & feel. is there a way we can show message using pop up from Java script code on UI.

Anshul,
Is the boolean validation rule able to be created in Salesforce?  If so, not JS needed since Skuid honors the SF rules.

@tom Scalza, unfortunately not, it has to be trigger in SF and would not be a good experience from UI point of view. we want to throw the error on click on checkbox…I have java script validation in place, all I need is how to show it on UI rather than showing in alert.

You could try this method.  
http://community.skuid.com/skuid/topics/trigger_popup_from_javascript

@ Tom Scalzo, thank you very much. This is what I was looking.