I’ve always wanted to live life efficiently. When I was in third grade I made a list of all the chores I had to do every morning (like make the bed) and timed myself doing them. I even made my mom assign quality grades to each task to make sure I wasn’t sacrificing on that margin for speed.

I don’t make my bed anymore, but I do grade a lot of papers and I like to give copious feedback. The returns to optimizing this process are big. That’s why I recently decided to try out several iPad PDF annotation apps to find the one that best fits my workflow.

My needs aren’t extreme. I mostly want to highlight, strike-through, and add colored text. Occasionally I want to underline, add a long note, or draw a shape. And since all my documents live on Dropbox, I want to easily sync whole folders. It turns out there are at least three apps that can do all of these things, but they have some important differences in how they get there. Here’s what I’ve found:

GoodReader 3.14

GoodReader has been my go-to annotation app for the last six months, and it sets the bar high. The only real annoyance is that you have to enter inline comments (i.e., use the typewriter tool) in a popup editing window before the app drops your words into the document. Once there, it’s easy to grab the comment (by holding a finger on it) and move or resize the text box. This is critical since you never know exactly where or how big the text box will be. You don’t have any control over the font for these inline comments and the one it chooses is cheesy typewriter, but I don’t mind.

Syncing folders with Dropbox is great although the sync button can get hidden way down in in the “Web Downloads” area are under a long list of “recent” downloads. In fact, the whole document management interface is functional, but messy and unintuitive–i.e., once you know your way around, you don’t waste a lot of time, but it’s never pretty and there is a learning curve.

One useful feature I haven’t found in the other apps is a Back button under the scroll bar that (obviously) puts you back where you were after you scroll somewhere else or move to a bookmark. This is great when you’re flipping between text and tables.

iAnnotate PDF 2.1

iAnnotate PDF has a clunky name and a cartoony interface. I think it’s been around the longest and it’s extremely configurable. People who use it swear it does everything they want but it takes a little work up front to set it up. I believe them. And when you add inline text, you do it in the page itself which is much more natural than typing into GoodReader’s disembodied text box.

On the downside, it’s been crashy for me. I’ve been using an original iPad, so maybe it’s more stable on newer hardware. It doesn’t have a scroll bar that lets you move directly to the end (or beginning) of your document. It doesn’t always highlight the spaces between words and I can’t get it to autocorrect when using the typewriter tool. But even if these things got fixed, I just find the ugly icons too distracting.

PDF Expert 4.0

Ah, we have a winner! PDF Expert is a breath of fresh air. It has everything I like about GoodReader (except the back button) in a package that’s just beautiful to look at. The document management UI is super-clean, fast, and intuitive. It even gives you thumbnails of the first page of each document. The icons in the document annotation UI are simple and classy. When browsing a pdf, the page turns are very fast.

On top of this, I don’t know how I lived without PDF Expert’s undo and redo commands. They not only keep you from inadvertently junking up your document, it means the UI doesn’t ever ask “Are you really sure?” when you delete something because you can always roll back to the previous state.

What’s not to like? Some people complain that it only opens one document at a time, but I find opening and closing to be fast enough that this isn’t a big deal. My biggest complaint (and it’s minor) is that you only have 9 colors to choose from for markup and they’re kind of brash. It’s like they were inspired by the available colors for Apple’s cheap Smart Covers.

Honorable Mentions

PDFpen has been around for quite a while on the Mac, and if Preview wasn’t as good as it was, I’d probably be using it there. But on the iPad, it’s the new kid on the block. None of the positive reviews on the app store compares it with the big three, and a few negative reviews say it’s crashy and has fewer features. It will probably improve over time, but considering it costs the most ($15) and seemingly does the least, I’m skipping it for now.

Notability is really a note-taking app that can also annotate PDF’s. When I’m in a meeting or seminar, I usually use Nebulous Notes and type right into a text file. If I have a copy of the slides or the paper being presented, I now take my notes right on them with PDF Expert. Notability is particularly strong with drawing, but I find even with my Cosmonaut stylus, the lag between moving the pen and seeing my picture is just too unnatural to replace pen and paper.

Bottom Line

PDF Expert is fantastic. I’m so glad I went through this exercise and have graduated from GoodReader! Of course, I could have just read Cynical Babblings’ recent review of same apps. I found it while I was in the middle of my evaluation process, and he’s much more thorough than I am. And he also likes PDF Expert best.

Update: On December 30, 2013 I wrote up my impressions of PDF Expert 5.0.