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Are there any commercially available fluorescent dyes that will bind only to double stranded DNA (not RNA, single stranded DNA etc.) for studying in vitro using confocal microscopy?

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Most of the dyes used for visualization bind with a much higher affinity to dsDNA. This would be SybrGreen, EtBr (although this will bind RNA as well). There is a pretty comprehensive website from Life Technologies about Nucleic acid stains that is worth a look.

There is as well a publication on this topic: "DNA Staining for Fluorescence and Laser Confocal Microscopy"

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