I’ve posted a couple of times about the misconception that all OA journals charge author-side fees, and each time I’ve mentioned the Kaufman-Wills study which found that 75% of the toll-access journals they examined charged author-side fees in addition to subscription charges. I thought it would be useful to compare author-side fees charged by OA and TA journals.
It’s easy to work out what OA and hybrid journals charge; BMC maintains a detailed list of publisher article processing charges.  Here are some examples:

What is much more difficult to determine is how much the average author is paying in author-side fees at toll-access journals, because the charge for a given article depends on number of pages and/or color figures, and in some cases also on whether supplementary information is included.
Below are a few examples; in each case for which I calculated a figure, I extracted the page and figure counts manually from a single issue. This is far too small a sample to be representative, but I’m just trying to get some kind of feel for the numbers. Further, the published figures I managed to find (indicated by footnotes) are consistent with my “calculated guesses”. Also, the NIH estimates (scroll to section L) that it spends “over $30 million annually in direct costs for publication and other page charges” and produces “roughly 50,000 – 70,000 manuscripts”, which means that the NIH is paying, on average, about $500/article in page charges. If around 8% of all new articles are Gold OA, that number goes up to about $543/article. If the Kaufman-Wills 75% figure is representative, then the average author-side fee being charged is $666/article, or $724/article if the %OA is taken into account. (Note that the %OA adjustment might be spurious and the estimated average slightly off, because we don’t know how much of the estimated $30 million is going to Gold OA fees.) Edit: according to Björk et al., only about 5% of all articles are available through Gold OA without an embargo period. Taking this into account, and assuming that the average Gold OA fee is triple the average TA fee, gives an average of $454/article, or $606/article on the Kaufman-Wills estimate.
Update: In comments, Peter Suber points out that the NIH has amended its estimates to $100 million/yr spent on author-side charges and 80,000 manuscripts funded — which brings the estimated average author-side fee to $1136; if only 75% of TA journals are charging such fees, then they are charging on average $1515. Much later update: see this post, I wouldn’t put too much weight on those NIH figures given the nature of the sources.
This section became way too cluttered, so I’ve put a summary here and the details are below:
journal ……………………………… average author side fee
PNAS ……………………………………….. $1446
Science …………………………………….. $1019
Nature ……………………………………… $1669
Cell ……………………………………….. $2031
Cell Cycle ………………………………….. $756
EMBO J ……………………………………… $2974
Mol Biol Cell ……………………………….. $1829 ¹
American Physiological Society (14 journals) ……. $1000 ²
Journal of Nutrition …………………………. $456
J Neuroscience ………………………………. $850 + color charges ²
Molecular Biology and Evolution ……………….. $922 ³
Molecular Plant-Microbe Interactions …………… $1275 ⁴
J Natural Res & Life Sci Education …………….. $400
¹ official figures, 2006
²official figures, current
³ official figures, 2008
⁴ official figures, 2000
The selection of journals is fairly random, just the first few that came to mind then whatever turned up when I was searching for things like “average page color charges”. They range from prestige to niche, and even the cheapest charge fees that amount to a significant fraction of Gold OA author-side fees.
It would be very interesting to extend this half-baked pilot study, but I think it would also be unavoidably labor intensive. Except for rare cases where publishers provide the numbers, there’s really no way to calculate average author-side fees based on page and figure counts except by doing those counts for a representative sample of issues in each journal. (Perhaps a passing statistician could help me figure out what would constitute a representative sample — perhaps sqrt(issues/year)?) Then you have to select which journals to investigate — perhaps high, middle and low ranked journals in a handful of broad categories? Finally, it’s pretty slow going, so I don’t think Mechanical Turk would be cost effective for this job — even if you could solve the problem of giving Turkers access to the journals. In the end I think you’d have to inflict the counting task on some hapless grad student or intern, who would probably find it easiest to sit in a library with a stack of journals and a spreadsheet.

—————————————-details of “calculated guesses” and official figures—————————————-
PNAS: $70/page, $250 for supplementary information, $300 per color figure or table

In 2004 Cozzarelli et al. suggested that around $2000/article would be needed to cover PNAS’  costs without subscription income.
Science: $650 for the first color figure, $450/color figure thereafter

Nature: £735 ($1072) for the first colour figure and £262.50 ($383) for each additional figure (note: “Inability to pay this charge will not prevent publication of colour figures judged essential by the editors”)

Cell: $1000 for the first color figure and $275 for each additional color figure.

J Neurosci: $850 for regular manuscripts, $450 for brief communications, color figures are free “when color is judged essential by the editors and when the first and last authors are members of the Society for Neuroscience”, otherwise $1,000 each.

Landes Bioscience (all journals): four pages free, then $80/page; $340 for the first color page and $150 for each additional color page (in print — color is free online)

EMBO J: $250/page over 6 pages, plus color charges: $650/figure for the first three figures, $432/figure for the next two, $2928 for six figures and $326 per additional figure thereafter.

Molecular Biology of the Cell: according to the Am Soc Cell Biol, in their 2006 publication “MBC and the Economics of Scientific Publishing” (available as a pdf from the linked page):

The average article published in MBC in 2006 was 11.7 pages long and included 2.9 color figures. With the 20% discount on page and color charges now offered to ASCB members, publishing such an article would cost the author $1,829.

(Regular ASCB membership is $130.) Interestingly, the same publication gives the following details of budgeted (projected?) journal revenue for 2008:

I don’t know how similar that breakdown would be for other journals, but it’s interesting that subscription revenue is roughly equal to page OR color charges — meaning that the average author would pay about 50% more if the journal switched to full cost recovery from author side fees.  This would put MCB’s author side fees roughly on par with those charged by the top two PLoS tiers.
The American Physiological Society’s Author Choice (hybrid OA) fee is $3000 for review articles and $2000 for research articles; according to their FAQ this is because:

For research articles, the Author Choice fee was determined by calculating the real average cost ($3,000) of publishing an article in an APS journal, and subtracting the actual average amount already paid by authors in author fees (page charges and color fees). The Author Choice fee for review articles is $3,000, because there are no other fees paid by authors of review articles. The Author Choice fee was designed to completely cover the cost of publishing an article.

which indicates that the average author-side fee for the 14 journals published by the APS is $1000.
Journal of Nutrition: in this editorial, AC Ross gave some figures regarding costs:

On average, each published page costs about $465, and pages with color, $1300! Each published manuscript costs, on average, $3233. Page charges (starting at $70) and color charges to authors ($400 per figure) are only a fraction of the actual costs of publication. Institutional subscriptions remain a key factor in the financial success of professional society journals like JN.

Page charges are currently $75/page for the first 7 pages and $120/page thereafter, and color charges are still $400/figure.

Molecular Biology and Evolution: in the 2008 Editor’s Report (pdf available here) the Society for Mol Biol and Evolution provided the following figures for MBE in 2008:

Current charges are $50/page plus $450 per color figure, giving an average cost/article of $922.
Phytopathology and Plant Disease: $50 per printed page for the first six pages and $80 per printed page for each additional page for members of The American Phytopathological Society and $130 per printed page for nonmembers. In addition, there is a $20 fee charged for each black-and-white figure or line drawing. Color charges are $500 for the first illustration, $500 for the second illustration, and $250 for the third and each subsequent color illustration in one article.
Molecular Plant-Microbe Interactions: $150 for the first 6 pages, $150/page or fraction of thereafter; Color charges are $500 for the first illustration, $500 for the second, and $250 for the third and each subsequent color illustration in one article. In addition, there is a $20 fee charged for each black and white figure or line drawing.

(Regular membership in Am Phytopath Soc is $76.)
Journal of Natural Resources and Life Sciences Education: $350/article, $10 per table and $10 per figure plus $100/color page (print only; color is free online).