[SalesForce] Using bootstrap timepicker/datepicker in visualforce

Your command button action will execute regardless of the javascript outcome, they don't go together quite well. What I would suggest is, to have a normal html input button from which you'll trigger your javascript validation function, then from within there call an apex action function that will call your apex method. Something like this:

<apex:form>
    <script>
        function validate()
        {
            if (true)
            {
                validateInApex();
            }
            else
            {
                // something else
            }
        }
    </script>

    <apex:actionFunction name="validateInApex" action="{!validateInApex}" rerender="someSection" status="loadingStatus"/>
    <input type="button" class="btn" onclick="validate();" />
</apex:form>

Per Jeff Douglas's ROLL YOUR OWN SALESFORCE "LOOKUP" POPUP WINDOW blog post, one way to do this is to simply create a dummy instance of an object that has a relationship with the one you want to perform a lookup on, and then use the appropriate property of that instance as the value of an inputField.

From his post:

MyCustomLookupController

Here's the Apex controller for the record you are either creating or editing. This is an extremely simple controller that just creates a new contact so you can use the lookup for the related account field.

public with sharing class MyCustomLookupController {

  public Contact contact {get;set;}

  public MyCustomLookupController() {
    contact = new Contact();
  }

}

MyCustomLookup

[ ... lots of code omitted; see the original post for full content ... ]

<apex:inputField id="Account" value="{!contact.AccountId}"/>

This is an ugly, hacky solution, and I'd hoped to find something cleaner, but it works. It'd be even uglier if you didn't already have an object with a field of the right type; in that case, I guess you could create a custom object whose entire purpose was to be used for this hack.