tl;dr? Start with Nuance PowerPDF Advanced.
I evaluated OCR software in Dec 2014 in prep for a big project - OCR on millions of English-language pages done in batches. If you're willing to spend a few hundred dollars you have many options; trial versions can get you thru if you only need to convert a few hundred pages.
Many software packages want to load all the input files, do OCR and coalesce the mess into a single output. IMHO this is dead wrong, I have no idea who would want that. I was looking for true batch: one output file for each input file, unattended operation, don't stop for anything, give me a detailed report at the end. Spoiler alert: I didn't find that.
Packages in alphabetic order follow. Prices shown below are list but discounts abound. Take my comments about accuracy with a grain of salt; your inputs will not be the same as my inputs so your mileage will certainly vary.
ABBYY Finereader 12 Corporate: $400. Batch feature is called the "Task Manager" and it's on the Tools menu. It will process files from a folder, including subfolders; it will happily create a separate output file for each input file. It does not seem capable of preserving the input folder hierarchy; all output files went to the same output folder. The accuracy was high in my tests, yet still the lowest of the packages I've listed here.
Adobe Acrobat XI: $300. Batch feature is called "Text Recognition/In Multiple Files" which can be found by clicking on Tools (third toolbar, top right side of the main screen). Processes subfolders, one output for each input. Stops and puts up a prompt if it finds a password-protected file. Does not preserve input directory tree by default; can do so by writing output to same folder as input. Accuracy was quite good in my tests.
Nuance OmniPage Ultimate (aka v19): $500. Batch feature is called "DocuDirect" and it's a separate program that comes with the package. It will process folders and subfolders; if you select the features just right, it will preserve the input directory tree in the output area. One output for each input. Stops and demands a password for a protected file. Seems to take excellent advantage of multi-core processors to run tasks in parallel. The accuracy was excellent. But stability of the batch processor is poor; a fuzzy document will stop it in its tracks, never to recover, derailing a batch with ease.
Nuance PowerPDF Advanced v1.1 (successor to OmniPage Ultimate): $150. Batch feature is called "Batch Converter" and it's reachable from the main program under the Advanced Processing tab. It will process folders and subfolders, preserving the input structure in the output. One output for each input. Will use multiple cores, but not aggressively; what that means is I could not get it to saturate a multi-core host. Accuracy is excllent, as good or better than OmniPage. Bad or fuzzy files did not cause it to hang. The batch processor writes (shock) a plain-text log file to the output directory.
ReadIris Corporate 14: $600. Batch feature is invoked by the "Batch OCR" item which is revealed by clicking on the "From Files" button on the main screen. It will process folders and subfolders, one output for each input, and by default the output directory structure matches the input directory structure. Stops and demands user input on an invalid file; processes without further complaint all protected documents apparently by OCR-ing the image. The accuracy was very good, on par with Acrobat.
On my desktop machine (only dual core), with my chosen inputs, every package required at least 3 seconds to process a page; some took more. Might be able to drive this down on a machine with more cores.
Gotchas abound, be sure to plan for them: invalid PDFs (some packages halt), password-protected PDFs (some packages halt, others convert anyhow!), and rotated pages (landscape instead of portrait). If you want the batch to run thru to completion, you have to prep the input area for these packages Very, Very Carefully. Look into the GhostScript package's print-to-PDF feature for a way of removing protection from PDFs.
Running large batches can lead to memory-exhaustion and hanging problems, even tho it should not (argh - probably memory leaks). If you're doing any kind of automation at all, a big problem is discovering after the fact what really happened - which documents could not be processed, which failed during processing, etc. It's like the desktop software people never heard of something called a "log file".
Finally getting support, even as a paying customer, is pretty difficult for these mass-market packages. For example I complained to one esteemed customer support rep about a package (which shall remain nameless) hanging for some large inputs. I waited 36 hours before giving up :). They sweetly suggested limiting the batch size to 300 documents. That was just completely unacceptable to me, but hey it got that support ticket closed dang quick, right? And that's all that matters, right? Sigh.