Getting back on topic....
So the curent evernote client options for Linux are:
Everpad - It's OK if you have a few notes I guess but as already mentioned, this just dumps all of your notes into one big mess. No stacking, no filtering by notebooks. On the positive side, there's a unity Lens for Ubuntu users.
Nixnote (formerly Nevernote) - Of the 2 native clients, this is the best choice. It's pretty much has all the featues and even allows you to edit the HTML. However, my experience is that this thing is VERY slow. Also, the GUI is simply ugly. If there are any UX designers out there using Linux, please donate some time to help out with this. There is a new v2 alpha release which does have an improved GUI but I couldn't get it to sync my account. I always keep an eye on this app but so far, it hasn't been up to par with the windows client.
Windows client running through WINE - In my view, this is the best way to use Evernote in Linux. If you need help installing in WINE there's a lot of help tutorials on this - just google it. If you are a complete noob to WINE and want the simplest way to install it, I would recommend purchasing the comercial version of WINE called "Crossover". It's what I use. The biggest downside in my view is that it occasionally crashes on start. If this is the case, you have to kill the wine process and restart the application. One other downside (for people not using MS Office) is that it doesn't seem to integrate with LibreOffice - this means that if you have a word doc in a note and click it, LO or whatever you are using for doc/x files will not open (same for excel and powerpoint). In Crossover, I just installed MS Office along with Evernote.
EDIT: there was talk in the past about Evernote releasing an offline webapp. It would be great to see Evernote release a packaged app for Chrome. I think this could then replace alll of the above
Update: Since version 4.6.6.xxx was released, I have had MAJOR issues getting Evernote to run in WINE More often than not, it crashes at start. Previously, this was only occasionnal behaviour. I really wish Evernote would just expand the Web client to allow offline editing, then we wouldn't be discussing any of this.
UPDATE 2: the kind folks at codeweavers suggested I run the application in a separate bottle ( I had Evernote installed in my Office 2007 bottle). After doing this it's working again.