Well, I'll tell you. My system works like this:
The Grand Overview
Monthly Spending Plan / Budget
For all that I love about Quicken, I absolutely despise its budgeting setup. It's cluttered, nonsensical, and useless to me. So, to budget (as well as monitor in real time) my spending for each month, I use a slightly-modified version of my Excel Spending Plan (v2.0). You can download it from the near-bottom of my Excel financial spreadsheets page. And more details can be found at my Spending Plan page.
I don't have a specific spreadsheet that I use to track my Emergency Fund. However, I do keep most of my E-fund (say, 90% of it) in its own account at Emigrant Direct (review). Any transactions that affect my Emergency Fund get logged/tracked in Quicken, as noted above, and I can always see its balance right there in my Quicken toolbar.
I use ExcelGeek's Freedom Account spreadsheet to track my Freedom Account and all its subaccounts and balances. I keep my Freedom Account funds at ING DIRECT (review), in an account that's separate from everything else. If you've never heard of Freedom Accounts before, or if you're just not sure what exactly they can do for you, head over and check out my Freedom Account page.
What combination of software (and/or notebook paper!) do you use?