I am absolutely addicted to Evernote. It has completely changed the way I keep myself organized. EVERYTHING I encounter goes into Evernote and everything gets tagged. Although I love the system, in the beginning I found it difficult keeping up with my note tagging responsibilities. This made my tags less useful because I could not rely on the information they returned when I searched them. To solve this problem I developed what I think is a unique method for tracking untagged notes.
The first step was to prefix each tag with a two letter prefix which signified the tag "type." For instance, all of my tags which represent the subject of a note begin with "SU)". So I have "SU) Sales," "SU) Negotiation," "SU) Management," etc. Likewise, all of my tags that represent the companies mentioned in my notes begin with the prefix "CC)". So I have "CC) Acme Enterprises" and "CC) XYZ Company" etc. I created a group of tags for each of the following categories: subject, company, next action needed, and priority. Each category has its own prefix.
Once all of my tags were renamed to include their type prefix, I created a saved search to find all notes which do not have a subject tag. For me, this custom search looked like [-tag:SU)*] (without the brackets). Likewise, the custom search for finding all notes without a company tag look like this [-tag:CC)*] (without the brackets). I created a saved search for each category of tags.
Now, periodically I click on these saved searches and retrieve all of the respective untagged notes and I have a tagging party. This method is easy to implement and it will help keep your notes properly tagged. So, if you also use Evernote and you are a fan of tagging and being organized, I hope you find this tip useful.