Apple - What OS X and iOS software combination tracks finances?

MoneyWell

MoneyWell is personal finance software that increases your wealth while reducing your debt. It does this by wrapping the tried and true envelope-budgeting system in a beautiful, modern interface.

They explain the features better than I do but it is actively supported by a great developer. The companion app for iOS is MoneyWell Express.

GNUCash:

Is a personal and small-business financial-accounting software, freely licensed under the GNU GPL and available for GNU/Linux, BSD, Solaris, Mac OS X and Microsoft Windows.

Designed to be easy to use, yet powerful and flexible, GnuCash allows you to track bank accounts, stocks, income and expenses. As quick and intuitive to use as a checkbook register, it is based on professional accounting principles to ensure balanced books and accurate reports.

You Need A Budget:

You can connect to your bank and download transactions, and display those transactions and your budget in a simple, easy-to-understand interface that helps you determine quickly how well you're doing sticking to your budget and saving for your financial goals. YNAB is noted by a number of its biggest fans for not obfuscating your finances and its own tools like other tools: it's not difficult to just jump in and start tracking your money. You can try the app for 7 days free, but after that it'll set you back $59.95.

Stash:

A free/open source, fast, simple personal finance app for Mac OS X.

iCompta:

An Application that lets you manage your personal accounts with ease. It also offers full synchronization between the Mac and iOS versions, enabling you to enter transactions wherever you go.

Money Plus:

A finance app that approaches the problem of organizing your finances through simplified methods. It’s easy to enter transactions and repeat transactions, plus you get to see your progress through five different windows: Overview, Daily, Categories, Budgets, and Graphs.

Squirrel:

Provides you with powerful tools to analyze, control and keep track of your spendings.

Money:

A powerful, comprehensive, and intuitive system designed to help you keep control of your financial life. Oversee your account balances, track investments, keep budgets, and manage your bank accounts, credit cards, loans, investments, assets, and cash.

Please note however that many of the Apps mentioned above are Premium products and not freeware.

A comprehensive list of financial Apps available for Mac users can be seen here.

Splashmoney

Manage your money anytime, anywhere. Connect to your online bank from your desktop computer or wireless handheld and download transactions directly into SplashMoney. Create budgets and then track and analyze your spending with customizable reports and charts. Synchronize your handheld with your desktop computer to stay on top of your finances whether you're at home, on the road, or in the office.

I've used Splashmoney since the Palm OS days, and I've stuck with it mainly because it handles direct OFX downloads from my various banks.

EDIT: I should add that Splashmoney also handles QIF imports.