I'm sure there are many ways to do this, but here's how I'm using Evernote for GTD and it seems to work pretty well for me. I do things a little differently depending on which of my two Evernote accounts I'm using (I have one personal and one for work to keep all that information separate). Just to avoid some typing the accounts will be referred to as PENA (personal EN account) and WENA (work EN account). Also note that I use the Windows client for most of my EN interaction.
Setting up the GTD tags (contexts)
I have a tag called GTD under my projects tag and under it are all the tags that help me organize tasks:
Within contexts on my PENA are things like @email, @home, @phone, @work, @errands, @[person's name here] and others. For my WENA I generally don't have anything but the @[person's name here] tags under contexts because the location context is pretty much moot (it's all @work!).
For my WENA, under my projects tag I also have all the projects that I work on as tags and in some cases, for projects with lots of aspects, I will have subtags for those aspects such as the version of the project I'm working on and the different teams I have to integrate with and anything else that gets a large number of tasks such as fixes for cross-browser compatability (the bane of your existence as a web developer). These project tags are not specifically just for GTD use so that's why I don't group them under contexts. Here's a screenshot of a fictional project with only a few aspect tags to give you the idea:
Of course, you may not be a developer like me but every project you work on probably has some kind of sub-divisions to it. Being able to filter by those often makes it a lot easier to stay on target or to pull up information when you have to communicate with someone else about your project who only deals with that aspect of it.
I create a new task in a note by pressing the space bar in the new note so that it will let me edit the note title (a lot of times I don't even bother with putting text in the note itself unless there is more information or I'm doing a note that is a waiting for to indicate what the dependency is). After entering the task in the title field, I add the GTD tag like next action, the main project tag, the project version tag and any of the project aspects necessary. Many of my tasks are from bug reports so I can't really phrase them as actions (since I don't know how to fix the problem when I make the task), but when possible I do try to use that GTD practice and make it a more explicit explanation of what needs to be done.
For tasks that have a hard deadline I use the Subject Date field to enter that (right click on the note and choose Attributes). The Subject Date field shows up in the list view for notes and they can be sorted by that when needed. I will also add a tag of expires so that I can filter out only notes with hard deadlines.
For my WENA when I'm done with the task, I just remove the next action tag and put a done tag instead. It's nice because I then have a record of when the task was finished (the note modification date) and can then pull up a list of stuff I knocked out that week for my status reports by doing a search. For my PENA I usually just delete done tasks but sometimes I keep them.
Making GTD work for me
The real power in GTD in Evernote comes from the saved searches and ability to filter by tags. Most of the time I just want to review my next action list for the project and version I'm working on so I will set up a search for the project tag and next action.
I save this search as something like "ExampleProject v1.0 todos". Then when I need to review what's outstanding I will click on that search and I can CTRL-click on the project sub-tags to filter the list by team/feature set or waiting for tag for status meetings.
I save a search like this to pull up my done tasks for the week to transfer to status reports:
These searches include the version of the project I am working on (the EPv1.0) and will need to be replaced once that version is no longer the current one. If your project doesn't have versions or phases then that's one less tag you have to worry about.
To view items with deadlines you can't really use a saved search because for some reason the subjectDate search param doesn't except week like createDate and update do. But you can still search for them like this (notes in my project where the deadline is between May 20 and May 23, 2009):
I also create searches for my PENA for things like my @errands tag so I can call it up on my phone whenever I am out and have an instant list of stuff I need to take care of.
Making GTD on EN even better
I have a wish to be able to export my GTD notes to an Excel spreadsheet for my WENA so I can more easily share them with my non-EN using managers and teammates (to build a task list and timeline, etc). I am thinking of writing an app to do this but it's a matter of time. The export features that EN has now to text or HTML don't export the note titles (which seems rather odd to me) so it's unusable for anything like that. If I could get that working I would never have to build another status report in Excel again and that would make me happy.
The other feature I would like is to be able to save configurations of the list view per search. So, for instance if I saved the search with the Subject Date column moved over next to Creation Date and ordered by Title instead of date then it would be nice if it could return to that configuration the next time I viewed the save search. In most other circumstances I prefer the columns and sort to be another way.