You will need to query the attachments table for all attachments whose parentId = your custom object IDs.  The code is from something I have in development right now and is bulkified.

List<Attachment> atchmnts = new List<Attachment>(); 
		atchmnts = [Select a.ParentId, a.IsPrivate, a.Name, a.IsDeleted, a.Body, a.ContentType, a.Id From Attachment a where a.ParentId IN :trigger.new];

Once you have the attachments, you can create a maping of the IDs to Sets of attachments so that you can create the emails for each custom object and loop through the set of attachments and add all attachments to the email.  There may be a better way to add an attachment to the set, but this works for me.

Map <ID, Set<Attachment>> attachmentMap = new Map <ID, Set<Attachment>>();
		for(Attachment a : atchmnts){
			if(attachmentMap.containsKey(a.ParentId)){
				Set<Attachment> aSet = attachmentMap.get(a.ParentId);
				attachmentMap.remove(a.ParentId);
				aSet.add(a);
				attachmentMap.put(a.ParentId, aSet);
			}else{
				Set<Attachment> aSet = new Set<Attachment>();
				aSet.add(a);
				attachmentMap.put(a.ParentId, aSet);
			}	
		}

 For me, this is a trigger on the opportunity, so now I loop through all of the opportunities in the trigger and create the emails (o.id is the id of the opportunity in this iteration of the loop). The code below is for adding the attachments to the email.

if(attachmentMap.containsKey(o.id)){
    //Declare a List of attachments for the mail 
    List<Messaging.EmailFileAttachment> a = new List<Messaging.EmailFileAttachment>();
					
	//add all attachments to the email
	for(Attachment att : attachmentMap.get(o.id)){
		Messaging.EmailFileAttachment efa = new Messaging.EmailFileAttachment();
		efa.setBody(att.Body);
		efa.setContentType(att.ContentType);
		efa.setFileName(att.Name);
		efa.setInline(false);
		a.add(efa);
	}	
    mail.setFileAttachments(a);
}

Hope that helps.  As far as Notes, I belive you can do something similar by querying the Notes table.