I have a paper for review and I would like to include comments (on clarifications/suggestions/errors) over specific paragraphs or statements.
What are some ideal software resources that could help reviewers? I would prefer them to be Linux-based.
However it's more likely that you have a PDF only. In that case, you need a PDF annotating package. A free cross-platform solution is Xournal, which runs on windows/linux (and maybe Mac).
Update: (by @atiretoo)
One issue to be careful with providing comments on a pdf or other document is maintaining anonymity. Adobe Acrobat (and probably other software), automatically flags your annotations with information about you unless you are careful to remove that from the document before commenting.
The approach taken by many reviewers (myself included) is to simply reference the page and line number, or to insert a copy of the statement in question in the referee report, e.g.:
On page 7, line 6, the word "mispell" should be "misspell".
This is probably the easiest approach if the number of such comments is not too large, since it doesn't require any extra software and doesn't require the authors to search through the PDF for your annotations.