I track mine in multiple different excel spreadsheets.
1) Trip Report
* Tracks what banks I visited
* Tracks what I picked up or cashed in while there
* Tracks what I found in what was picked up by denomination
* I use this spreadsheet to copy and paste what I find into my posts
* Calculates find percentages of various things like wheat pennies, silver dimes, etc.
* Keeps track of my total finds for the year (I start a new spreadsheet every year).
2) Total found - year
* This spreadsheet has pages that help me track how many of each denomination/date/mintmark/variety I found
* I create a new one every year
3) Tracking list - year
* Similar to the Total found except that I only enter 1 if found and 0 if not.
* I use it to track what percentage of a complete set of any particular variety I found in a year.
* Technically, this spreadsheet is somewhat redundant with #2 and I should probably combine the two...just haven't done so
* I also list non-canadian foreign coins found including listing the number of any particular date if multiples are found
4) Tracking list - lifetime
* The same as #3, except it tracks my finds over my entire lifetime.
* I also list each unique non-canadian foreign coin found, but limit the list to not include multiples.
5) Overall collection
* I use this to track how many of any particular coin I have in my collection.
* It includes pages for all the different US coin denominations and includes all mintmarks and intentional varieties as well as some of the errors.
* It also includes a place to enter how many slots in books that I want to fill.
* It does a bunch of calculations showing me how many of each coin I still need to complete my desired collection goals
* This combines any coin purchased with all my finds.
* It also includes pages for each denomination of US currency, it lists which federal reserve branches had star notes in each series.
Prior to 2012, #2 through #5 were primarily US coins with only a stub for Canadian coins. For Christmas this past year, I got a copy of the Charlton Standard Catalogue for Canadian Coins 2012 and created spreadsheets #2 through #5 for Canadian coins as well.
I keep meaning to write a database application that allows me to essentially combine all my spreadsheets into one, simplify the UI, and spit out reports that I can post directly, but... I just haven't taken the time to start yet.