Well, I'll tell you. My system works like this:
The Grand Overview
I track all accounts, balances, and financial transactions in Quicken 2006 Premier Home & Small Business. This is also where I categorize my past and current spending, as well as monitor my net worth, assets and liabilities, and investments. I also use it to track all my small-business (namingly, this website and my wife's jewelry/craft business) inflows, outflows, and accounts. Quicken is also a tremendous tool for handling all tax-related items and accounts. I use the heck out of it for this. Is Quicken pricey? Yes, the fancier versions can be. Does it require a fair bit of learning time? Yes, though this also depends on what version you get and what you want to use it for. Would I give it up? No way. Not a chance.
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.
Emergency Fund
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.
Freedom Account
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?