I use Evernote as my software package of choice for managing to do lists, as well as for archiving the little bits of data I need here and there. Following (somewhat loosely) David Allen’s Getting Things Done methodology, I’ve created the following notebooks in my evernote account.
I placed numbers before some of them so that they would sort in an intuitive fashion on the desktop and on the Android, as those are the two places I use the software the most (the droid gets most of the writes and updates, the computer is where most of the reads happen). Here are the notebooks I created:

• 0-Inbox
• 1-Now
• 2-Next
• 3-Soon
• 4-Later
• 5-Someday
• 6-Waiting
• 7-Done
• Cabinet (this is actually a notebook stack, in Evernote parlance)

My default folder is 0-Inbox. I’ve rigged all of email accounts up so that they have my evernote inbox as a contact. That way, I can quickly just shoot an email over when I need to add something the inbox folder. I also use the Evernote Web Clipper browser add-in, with this as a default folder. Essentially, 0-Inbox is a dumping ground for things I haven’t prioritized, organized, or vaporized. It is simply meant as a place to capture information so that it can be handled later. This can be everything from tasks that need to be completed to articles I want to read, to bits of reference information I don’t want to lose. I’ve also rigged up rules in my email accounts to forward certain emails to this box based on a filter. For instance, if my wife sends an email with “Grocery List” as the title, it shoots straight over to evernote. I generally still alter the list before I take it to the store (her lists are stream-of-consciousness, whereas the grocery store in sections, plus I need to check things off), but that at least gets it where it is accessible on my phone if nothing happens to be going correctly that day.

Twice a day, I triage 0-Inbox. Each item goes into one of the numbered folders above, or into a subfolder of cabinet (depending on subject), or is entered into some other system. Items that have to be handled immediately go into 1-Now; the other numbered boxes indicate the priority of the item. I used folders in this case because items are only at a single level of priority. I also tag items. Tags are one of the secret dirty tricks of evernote. Here is the scheme I used to tag things. I name the tags in such a way as to cluster tags of the same type (again, I do a lot on my phone, so this makes it easier).

1. If it’s associated with a person or company, it’s prefixed with an underscore. For instance, I have tags for “_CellJournalist” and “_Dad”.
2. If it’s a project I’m working on, it’s prefixed with a #. So I have tags for “#HomeRepair”, #Contact
3. If it is something that can only be done at a specific location or with a specific piece of hardware in hand, it’s prefixed with an @. For instance, I have tags for “@Home”, “@Computer”, “@Dev”, “@Phone”, “@Work” etc.
4. If it’s just a general category of non-action items, it goes in a folder under cabinet. I do have tags for specific sorts of things that aren’t todo items, but these aren’t prefixed with anything, and truth be told, I rarely use them, as evernote’s full text search is good enough.

Basically, for each task, I assume that there are several bits of information you want as metadata. Who, what, when, and where (why and how go in the note itself if needed). For all but the “when” question, it’s resolved to tags. For the “when”, I place the items in an evernote folder. Notes can have any number of tags, but can only reside in one folder. This facilitates my processing of items I’m tracking by priority.

When I triage 0-Inbox, I tag things and move them to the correct folder. Work starts AFTER 0-Inbox is cleared. I do it first thing in the morning and at the end of lunch. Many people I know do this work in the bathroom using their smart phone. That’s fine too, just don’t combine that practice with doing it at lunch from the same phone (ewwww…). When 1-Now is empty, I quickly grab items from 2-Next and move them over, then begin working. You should always have items in those two folders. You should move items into and from 2-Next and beyond only during your triage period (this keeps you from wasting time crawling back through all your notes looking for something to do). There is NO separation here between work and regular life items (although you would separate the execution of those items into work and off-work hours, obviously). One of the big keys here is to have a single, authoritative source of what you are up to (you may need to update other systems, but this is the one you refer to when you are figuring out what to do next). The beauty of the Getting Things Done system is that it takes all the various things you have to track and puts them in a single system, so that they no longer take mental focus away from you.

Now, with these set up, you can quickly create named searches in Evernote. There are more thorough examples here. You might, for instance, set up a custom search for things you can do on your cellphone for the next time you are stuck in line at the grocery store behind the person who is buying an entire cart worth of food using pocket change. Here are some simple ones to give you a rough idea of what you can do with the syntax (the part after the arrow is the explanation):

1. notebook:”1-Now” tag:”@Work” => would give you a list of all the items currently pending for work.
2. tag:”_Dad” => Would give you all the notes related to Dad, so you could remember if you owe him a beer, or remember if you said you would bring something to him next time you came down.
3. tag:”@Computer” -tag:”@Internet” => Would give you a list of all the computer tasks you have that don’t require the internet. This search returns nothing for me and never has returned anything, but your mileage may vary. Be aware that there is a “-tag” operator, but not a “-Notebook” operator. As a result of this, it’s best to tag completed items as “Done” or to simply delete them if you don’t need a record. I’ve asked the Evernote folks about this; I hope they fix it someday soon.
4. tag:”@Phone” => When you get to the part of your day where you need to make phone calls, this search will turn up the list of people you need to call. I tend to batch these operations because I loathe being tethered to the phone and would rather get the unpleasantness out of the way all at once, in much the same way as if I were on fire I would prefer to burn up quickly.

Now, the other thing besides a triage and organization process that you need as far as documents go, is that you need some way to reference stuff elsewhere. For digital docs that aren’t sensitive, I stick them in Dropbox. That way they are available and I can simply put it in the note that the relevant files are in drop box. You might consider making a tag for “@Dropbox” if you do this. With physical files and objects, you reference their location, or (in the case of some physical files that aren’t sensitive), you may want to scan them in to Evernote (they actually sell a special scanner for this – I haven’t tried it, but I’ve heard it’s nice). For sensitive things, like passwords, I use KeePass password safe with a very strong passkey that I change every few months. I store the keyfile in my dropbox. Highly critical passwords are not in there. Anything that touches a bank account is stored elsewhere, for instance, in an undisclosed location.

Now, there are a few items that help.

1. Many of the software products we use to track progress can also send email notifications. Send those to a gmail account, and then use rules to determine whether they are forwarded to Evernote and sent to 0-Inbox or not. I’ve done this with AgileZen and other products (including TFS….shudder). Just remember the rule. All kinds of things can put stuff in 0-Inbox, but ONLY you put the things elsewhere. That keeps a mess from growing somewhere else, with you finding out at an inopportune time.
2. Have specific times in the day for specific tasks. For instance, I code well between about 6:00 AM and 8:00 AM. I’m usually hyper enough from coffee by about 8:30 that I can fake being good with people and do well on the phone. By 9:30 or so, I’m ready to get back to coding. I run errands at lunch. From 1:00 to about 3:00, I’m about 50 IQ points low, as far as coding ability, but I can write well then, or do try to find bugs in software. Between 5:30 and about 9:00, I do equally well at writing and coding. I have constructed special searches for each of these time periods that show me a list of what tasks I have available to do during that particular time. So, it’s not just time management, but it’s also management of attention and capability. I should do the things I can do when I’m best able to do them, not in whatever block it occurs to me to do them. as tasks done efficiently still save time. When you have a productivity system that works well with the way you tend to do things and is mostly unobtrusive, you’ll stick with it.
3. I also use evernote to log my food intake, workouts, and meeting notes. These triage items go into other systems later, but this allows me to have a single point of capture so that I can reference things later if needed.

4. I do not always capture notes using evernote. I often do a quick and dirty email from gmail when I’m capturing things or I use the evernote web clipper. Data acquisition and sorting are two different things. I find when I try to organize stuff as it comes in that I end up missing things. It’s far better to do this organization when that’s the only thing you are trying to do at the moment, as it cuts down on the mistakes.
   Now, there are a few places where this approach is currently falling flat on its face for me. I’m working on these, but here they are.

5. Managing time-boxed things (such as calendar events). I pretty much still have to use google calendar to manage meeting times. I need the notification in advance or I’ll forget, plain and simple. I know evernote has notifications, but they aren’t as full-featured as gmail’s.

6. Data acquisition when operating a car is a bit of a pain. I generally try to avoid doing this, but sometimes you really need to record a reminder so that you don’t forget something critical. I know you can record voice notes in Evernote, so I’m probably going to try that. Nevertheless, I’ve yet to come across any speech-to-text technology that can understand Southern.
7. I have a proliferation of contexts. For instance, each client website I work on has its own @ tag. This lets me batch work for clients, but I end up with a lot of spurious tasks that I’m not in a context to handle. I think I can fix this with better organization, however.