Ok, here is my controller class that I am testing: 

global with sharing class InvoicePdfWsSample {
  /**
   * Default header height for invoice
   */
  private static final String DEFAULT_INVOICE_HEADER_HEIGHT = '100';
  
  /**
   * Default footer height for invoice
   */
  private static final String DEFAULT_INVOICE_FOOTER_HEIGHT = '100';
  
  /**
   * Webservice method that is called from a custom button to generate
   * an invoice PDF file using quote templates feature.
   * It generates the invoice based on:
   *     - The synced Quote
   *    
   * If the Opportunity doesn't have any Quotes, this method doesn't do
   * anything.
   * 
   * This method uses PageReference.getContent().
   *
   * @param oppsIdList {List<Id>} list of Opportunity Ids from where the method
   *           will generate the Invoice PDF.
   * @return {String} with an error message, if any. Blank otherwise.
   */
  webService static String generateInvoicePdf(List<Id> oppsIdList) {
    try {
      //From list to set
       Set<Id> oppsId = new Set<Id>(oppsIdList);
        //Get template Id for Invoice and url to hack pdf generation
       system.debug([SELECT value__c FROM Application_Properties__c where name='Invoice_Template_id']);
     String invoiceTemplateId = Application_Properties__c.getAll().get('Invoice_Template_Id').value__c;
      String invoiceHeaderHeight = Application_Properties__c.getAll().get('Invoice_Header_Height').value__c;
      String invoiceFooterHeight = Application_Properties__c.getAll().get('Invoice_Footer_Height').value__c;
      String quoteTemplateDataViewerUrl = Application_Properties__c.getAll().get('Quote_Template_Data_Viewer_URL').value__c;
      
      //Pre-validations
      //Invoice_Template_Id and Quote_Template_Data_Viewer_URL are mandatory 
      if (String.isBlank(invoiceTemplateId) || String.isBlank(quoteTemplateDataViewerUrl)) {
        String errorMsg = 'Invoice Template Id or Quote Template Data Viewer URL are blank, please review their values in Application Properties custom setting.';

        return errorMsg;
      }
      
      //Default values for invoice header/footer height
      if (String.isBlank(invoiceHeaderHeight)) invoiceHeaderHeight = DEFAULT_INVOICE_HEADER_HEIGHT;
      if (String.isBlank(invoiceFooterHeight)) invoiceFooterHeight = DEFAULT_INVOICE_FOOTER_HEIGHT; 

      //Iterate over Opps and generate Attachments list
       List<Attachment> attList = new List<Attachment>();
      for (Opportunity opp : [select Id,
                       (select Id, Invoice_No__c, QuotetoInvoice__c, CreatedDate
                         from Quotes 
                         order by CreatedDate DESC)
                  from Opportunity
                  where Id IN :oppsId]) {
        //No Quotes, no party
        if (opp.Quotes.isEmpty()) continue;

        //Synced quote
        Quote theQuote = null;

        //Try to get the synced one
        for (Quote quoteAux : opp.Quotes) {
          if (quoteAux.Quotetoinvoice__c) {
            theQuote = quoteAux;
           
          }
        }

        //No synced Quote, get the last one
      if (theQuote == null) return 'Select a Quote to Invoice under Quotes section';

        PageReference pageRef = new PageReference(
          quoteTemplateDataViewerUrl.replace('{!QuoteId}', theQuote.Id)
                        .replace('{!InvoiceHeaderHeight}', invoiceHeaderHeight)
                        .replace('{!InvoiceFooterHeight}', invoiceFooterHeight)
                        .replace('{!InvoiceTemplateId}', invoiceTemplateId)
        );
                      system.debug('opp.id.....'+opp.id);
                     Blob content;
                      if (Test.IsRunningTest())
                      {
                          content=Blob.valueOf('UNIT.TEST');
                      }
                      else
                      {
                          content=pageRef.getContent();
                      }             
        attList.add(
          new Attachment(
            Name = 'Invoice #' + theQuote.Invoice_No__c + '.pdf',
            Body = content,
            ParentId = opp.Id
          )
        );
      }

      //Create Attachments
      if (!attList.isEmpty()) insert attList;
      
      return '';
    } catch (Exception e) {
      System.debug(LoggingLevel.ERROR, e.getMessage());

      final String errorMsg = 'An error has occured while generating the invoice. Details:\n\n' +
                   e.getMessage() + '\n\n' +
                   e.getStackTraceString();
      
      return errorMsg;
    }
  }
}

Then here is my test class:

@isTest(seealldata= TRUE)
public class TestInvoicepdfclass {
    static testMethod void testpdfbutton(){
        
        // Pricebook2 pb = new Pricebook2(Name = 'Standard Price Book 2009', Description = 'Price Book 2009 Products', IsActive = true );
        // insert pb;
        Product2 prod = new Product2(Name = 'SLA: Bronze', IsActive = true);
        insert prod;
        PricebookEntry pbe=new PricebookEntry(unitprice=0.01,Product2Id=prod.Id, Pricebook2Id=Test.getStandardPricebookId(), IsActive= true); 
        insert pbe; 
        Test.startTest();
        
        
        integer csCount = Application_Properties__c.getAll().values().size();
        if(csCount<0){
            
            List <Application_Properties__c>  app= new List<Application_Properties__c> ();
            if (!app.IsEmpty() && app.size()>0) app.clear();
            Application_Properties__c cs1 = New Application_Properties__c(Name = 'Invoice_Template_ID__c', Value__c = '0EHj0000000LWh4');
            Application_Properties__c cs2 = New Application_Properties__c(Name = 'Invoice_Header_Height', Value__c = '100');
            Application_Properties__c cs3 = New Application_Properties__c(Name = 'Invoice_footer_Height', Value__c = '100')     ;
            Application_Properties__c cs4 = New Application_Properties__c(Name = 'Quote_Template_Data_Viewer_URL', Value__c = '/quote/quoteTemplateDataViewer.apexp?id={!QuoteId}&headerHeight={!InvoiceHeaderHeight}&footerHeight={!InvoiceFooterHeight}&summlid={!InvoiceTemplateId}'); 
            app.add(cs1);app.add(cs2);app.add(cs3);app.add(cs4);
            insert app;
        }
        Account acc = new Account (name='Acme');
        insert acc;
        Opportunity opp= new Opportunity (name='Testopp', Accountid=acc.id, CloseDate= date.today(), StageName='Closed Won', Pricebook2id=Test.getStandardPricebookId());
        insert opp; 
        
        OpportunityLineItem oppLine = new OpportunityLineItem( pricebookentryid=pbe.Id,TotalPrice=2000, Quantity = 2,Opportunityid = opp.Id);
        insert oppLine;       
        // insert quote
        Quote q= new Quote (Name='Testq', Opportunityid=opp.id, QuotetoInvoice__c= True, REP__C= 'AC', Pricebook2id=Test.getStandardPricebookId());
        insert q;
        //add to list
        List<id> oppids= new List<id> ();
        oppids.add(opp.Id); 
        
        InvoicepdfWsSample.generateInvoicepdf(oppids);
        Test.stopTest();
        
    } 
}

If you notice on line 32 of my controller, I put a check query and it returns this: 13:02:12:331 USER_DEBUG [32]|DEBUG|(Application_Properties__c:{value__c=0EHj0000000LWh4, Id=a07j000000J4xlQAAR})

But then on line 33, Im getting nullpointer exception on the same thing! How is this possible?
13:02:12:331 EXCEPTION_THROWN [33]|System.NullPointerException: Attempt to de-reference a null object