I'm currently using OneNote from Microsoft forto organize and keep record of most of my data, activities and notes. I'm using its online storage to have it automatically shared between my home desktop, personal notebook and office notebook. Unfortunately it has some limits (for example, no integration with eBooks) but it is the most comprehensive and powerful tool I've found.
I tried for a while also Evernote and, while its online sharing is quite better and it can be used on Android (my current mobile platform), it is not powerful as OneNote.