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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.

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If you have access to the LaTeX source, there are a number of packages that will help you. Some include todonotes and fixme.

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).

If you're on a iOS device, then Goodreader is a nice app that does annotations. There's always Adobe Acrobat as well. Both of these solutions are not free though.

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.

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    On Mac OS X, you can just use Preview. – David Ketcheson Jun 28 '12 at 9:07
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    Xournal is very nice. – David LeBauer Jun 28 '12 at 16:59
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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.

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    When I get back my own papers after review, I much prefer those that include a list of changes by position like David has suggested. That way, all of the suggested changes are in one spot and I am less likely to miss one. – Ben Norris Jun 28 '12 at 11:08
  • This is a good option, but how do we get line numbers if a pdf was provided? Esp. in IEEE format, it gets complicated - page 3, column 2, line X! – Bravo Jun 28 '12 at 15:55
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    Note that the GoodReader suggestion in the other answer (and other annotating softwares) will export the notes with line numbers, giving both this preferred format and a visual markup format on the PDF also. – mankoff Jun 29 '12 at 2:47
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    For journals which do not provide PDFs with line numbering, I usually indicate by both position and context. E.g. 'On page 7, top third of the page, in the sentence "In this work we will demonstrate the following nonobvious face" perhaps the authors intend to write "nonobvious fact".' – Willie Wong Jun 29 '12 at 11:01
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    For most typos, you do not really need to provide that much context or pinpoint a specific location. Using @WillieWong's example, this would be usually sufficient: "p. 7: nonobvious face -> nonobvious fact?". The authors can easily use the search tool in their text editor to find the right spot. – Jukka Suomela Jul 1 '12 at 11:57

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