I am a control freak. I freely admit it. None of my iPods are set to sync content automatically. If I want to add something, I'd rather go through the drag and drop routine. I'm the same way with my iPad
I've been using GoodReader for the PDFs that I like to carry on my iPad, but now that iBook handles PDFs, it has become my reader of choice. You can add files to both by the drag and drop method, but they do it in different ways.
For iBooks, select "Books" in the left column, then drag and drop your document in the right hand window. It automatically uploads to the iPad without going through a sync.
For something like GoodReader, select the iPad, click on the "Apps" tab, then scroll down to the bottom of the window. Click on the proper app, then once again drag and drop into the right hand window. Again, it automatically uploads without syncing.
Okay, why do I prefer iBooks for my PDFs? Because on multi-page documents, it will show me thumbnails of each page. Makes it easier to find just what I'm looking for within a document.