Here is one I have been contemplating using. Not sure but sounds like it may be what your looking for.
iAnnotate
This info pasted from their site which has a link to the app in AppStore.
Full-featured PDF reader: continuous-scrolling page display with all standard scroll/zoom gestures supported. Tap to show and hide the interface for fullscreen reading.
Tabbed PDF Reading: quickly switch between multiple documents. Tab setup and page locations are always remembered, whether switching tabs or quitting and returning to the app.
A complete annotation system: Text Notes, Highlight, Underline, Free-Form Drawing, Bookmarks, and more. Our easy-to-use interface allows you to view and edit your annotations without leaving the document reading view. Full-spectrum color selection allows you to set up your personal color system for annotations.
Fully Customizable Toolbars: reposition and resize, drag-and-drop to configure toolbar commands. Toolbars can be positioned on or outside the PDF view, and are optionally translucent.
Comprehensive document and full-library search: search your entire PDF library instantly -- results update as you type your search term. Forward and backward search result navigation.
Full PDF support: Copy-and-paste text, view existing PDF annotations, support for internal and URL links, and PDF outline/bookmarks support.
Desktop Sync: Easy synchronization with PDF documents on your computer.
Aji Support: integrated application help and tips, and top-notch email and forum support.