A.nnotate is the newest addition to this list. Instead of describing A.nnotate in detail here, though, I’m going to suggest you read a very thorough description of it — with screenshots — at The Make Use Of blog.
eMargin is a free tool developed by Birmingham City University in the United Kingdom. You can upload any text and have students annotate it, and the same text can be annotated by a closed group. In addition, you can “upload” a web address and annotate it, as well. The lay-out can be a bit funky with websites, but it’s still workable.
NowComment seems like a good tool for students to use when annotating online documents and they can see the comments of others, too (teachers can create private groups). The only way you can annotate a website is by copying and pasting it, and I’m not sure if that’s legal or not.
Diigo is a superior bookmarking tool (I use both diigo and delicous to back-up all of mine). My grip against diigo has been its requirement for a downloaded bookmarklet in order to annotate saved webpages. Recently, however, you can now annotate saved webpages without installing anything — you can highlight, make comments and share them.
Edji lets you upload any text and have readers annotate it with comments. You can make all the comments public to readers, or keep them private.
Prism also lets you just annotate text to upload, but in a very dynamic way.