Michael Davidson maintains an excellent family of websites, many sponsored by manufacturers, which are an excellent source of microscopy information:
The Molecular Probes Handbook - a good source of information on fluorescent dyes and small molecule reporters.
openoptogenetics - Optogenetics wiki site with good technical information
- FPbase- a good source of information on fluorescent proteins. Spectra viewer also useful for comparison of filter sets between different fluorescent proteins.
John Maloney has a very nice presentation on statistics and data analysis from the MIT IAP: Maloney.pdf
A nice primer on image analysis in ImageJ/Fiji: Analyzing fluorescence microscopy images
Brain Windows - A neuroscience postdocs posts, focused on brain imaging.
Austin Blanco's Microscopy blog - From one of Technical Instrument's former employees.
Labrigger - Blog that offers alternatives to expensive lab equipment
Kurt's Microscopy Blog - from the director of the NIC
Image.sc - Community forum for multiple open-source image analysis software packages where you can find answer to common problems and post questions to the community. The forum is very active and you can get help quickly.
Microforum- Community forum based on hardware, acquisition, and specimen-related question.
Recommended Books on Microscopy
Fundamentals of Light Microscopy and Electronic Imaging, Douglas B. Murphy: A good general purpose introduction to commonly used microscopy techniques, including fluorescence, phase contrast and DIC, and brief discussions of confocal microscopy and cameras.
Handbook of Biological Confocal Microscopy, 3rd ed., James Pawley, ed.: This is the book to get if you want an in-depth understanding of not just confocal microscopy, but the whole diversity of modern microscopy techniques. It's not a good introduction to the subject but it is a fantastic reference work with lots and lots of technical detail.