I was doing some looking around for the first time in sometime for what resources there might be for my genealogy online and I found some very interesting sites.
Family History Documents from Estonia This site has numerous church books within it and is a great way for me to confirm details of my ancestors. I am sure there is data there that my other sources over the years have not had. The site is big and will take a long time to go through.
Manors in Estonia - being a Baltic German noble, this site is very interesting. I found some pictures from my families old home Limmat there ( Lümandu in Estonian) I also found this site with pictures of the house in about 2004 - who they are and why they are there, no idea.
This site offers digital images of the pages of the various Genealogical Handbooks for the Baltic German nobility.