I've been a huge fan of Evernote for a couple of years. It is about the most flexible information storage application you can imagine. Information is stored as notes that can be collected into noteboooks for different topics. Each note can be tagged for fast searching.
Originally I started using it to help me organise tasks for very short term to longer term projects, but I quickly started finding more and more uses for it.
The best part is that the data is stored in the cloud and can be synchronised between desktop, laptop, tablet or phone. No matter where I am, I can retrieve information quickly or edit it.
The only downside is that Evernote have not produced a linux version of their software.

But the wonderful thing about linux is that there is always an alternative, and in this case it's called Nixnote. Although it's a little rough around the edges, Nixnote provides a lot of the functionality of Evernote and connects to exactly the same servers. That means I can use Nixnote on my linux desktop and laptop and use the Evernote app on my android phone to access the same data.
Now comes the sad part to this story. For a number of reasons, I have decided to leave the world of Ubuntu and go back to Debian (these are different version of the Linux operating system). When I converted my laptop I discovered that my beloved Nixnote wouldn't work properly. As I studied the error messages generated by the system I found that Nixnote relies on something called libssh 0.9.8, but Debian only supplies the more up to date libssh 1.0.0.
After trying a few workarounds, I decided to go over to the dark side. I downloaded the Windows version of Evernote and tried it under Wine, a program which gives Linux users the ability to run some Windows programs. Often programs run under Wine are unreliable, unstable, slow or just don't work. But Evernote works perfectly on my laptop. In fact it is so good that I have ditched Nixnote altogether on my desktop in favour of Evernote.
So I can continue my love affair with Evernote, whether I use the official apps or unofficial apps.