Annotater still only one that allows you to search within the PDF as far as I know. I use it to search my 15,000+ karaoke songs on my iphone.
I prefer Annotator for browsing large PDF files. In addition to searches, Annotater supports links and bookmarks within PDFs, so it's easy to jump around. Note: Annotater requires sharing software that only runs on Mac OS X.
I'm a huge fan of Annotator. Upload PDFs to the phone, then add annotations on the go, then sync them back to my mac and print out PDF with annotations with Acrobat.
To continue the alternation: I use Air Sharing I have Air Sharing loaded up with a bunch of PDFs RTFs and Word docs for reference, along with some useful downloads (Mac and Windows) that I recommend to clients. Instead of emailing them a link to a utility, we don't even need Internet: they can download it from my phone.