In the traditional way of handling submittals, there were numberous time consuming steps: log in the submittal, stamp the submittal with a 'received' date, stamp the pages of each copy of the submittal with the review stamp, review and mark up one copy, copy all the review comments to the other copies, prepare for mailing/delivery, add transmittal, update log.
Marking up the submittal can be done with a number of programs. On the Mac platform, 'Preview' has adequate tools. Evernote's 'Skitch' works well in both the Mac and PC worlds. You could use Adobe's Reader XI which now seems to have everything you need, including the ability to create custom stamps!
When you return the submittals, often the traditional review stamp is a stumbling block. We have combined the stamp with our 'Submittal Transmittal Form' to take care of that.
The last piece of the process is the log. A spreadsheet works the best because it can take any size that is needed. It rarely needs to be printed, so fitting it to a paper size isn't necessary. Print it with a plotter if it ever becomes necessary, otherwise just review the file. Over several projects you will develop a 'master log' that contains all the spec sections that normally have a submittal requirement. Copy the log from job to job and erase all the specific content leaving the spec sections as a kind of checklist of what needs to be submitted. You will find that additional rows have to be entered on every job, sometimes to accommodate a new spec section and other times to accommodate the second or third submission of the same submittal.
It goes without saying, but I will say it, SAMPLES don't work at all well using this Paperless Submittal process.