- Strip download watermarks ("Downloaded by Wisconsin State University xxx.xxx.xxx.xxx on January 12, 2017 13:45:12"). Many times, journals published by the same publisher do the watermarking similarly so you need write just one pdftk (or other PDF manipulation software) script for every journal under their banner. At worst, it's a one-script-per journal effort.
- PDF optimization. A lot of publishers produce un-optimized PDFs that could be 25% (or more) smaller with a completely lossless space optimization pass. This should save storage/network costs for access to individual papers and, more importantly, reduce the burden for bulk mirrors.
(I'd contribute the scripted passes myself if I had contacts within sci-hub.)