As an example of the former, Sheaffer lists "40% of the Amazon rain forest is threatened by global warming" as a false claim of the 2007 IPCC AR4 report. In fact, the claim is correct; the only error in the IPCC AR4 report was to cite the wrong source for the claim. The "Amazongate" charges originated with poor research by Richard North and were promulgated in a Sunday Times (United Kingdom) story by Jonathan Leake. The Times was forced to retract and apologize for the erroneous story, as described on the Real Climate blog (http://www.realclimate.org/index.php/archives/2010/06/leakegate-a-retraction/).
As an example of the latter, Sheaffer is correct that the IPCC WGII report on Himalayan glaciers was in error, as has been widely reported. I think it's important to distinguish between the three IPCC working groups--WGI, research on the physical basis of climate change; WGII, research on scientific, technical, environmental, and social aspects of climate change (e.g., vulnerability and adaptation); and WGIII, research on mitigation of climate change. It's my impression that the work in WGII has received more substantive criticisms than that in WGI, e.g., by Roger Pielke, Jr., who has complained about his own work being misrepresented by WGII, yet he supports the results of WGI [see, e.g., http://lippard.blogspot.com/2009/11/roger-pielke-jr-on-climate-change_07.html]). Cook's Skeptical Science site addresses most of the claims Sheaffer has made, in a numbered list sorted by recent popularity (http://www.skepticalscience.com/argument.php). As of this writing, it addresses 116 arguments from climate change skeptics, including the following from Sheaffer: global warming is due to the sun (#1), the weather hasn't warmed since 1998 (#7), we're heading into a new Little Ice Age is (#9), the "hockey stick" is broken (#18), the Medieval Warm Period was warmer than today (#56), the IPCC was wrong about Himalayan glaciers (#75), Michael Mann performed a trick in Nature to "hide the decline" (#77), and the IPCC was wrong about Amazon rainforests (#94).
[Not printed: P.S. I know that Robert Sheaffer promotes Joanne Nova's "The Skeptic's Handbook" on his website. The Skeptical Science website has criticized some of her arguments here: