You need CrossOver... It's "Fine Wine", i.e., Wine polished into an effective tool, complete with a GUI manager, DLL wizard, automated installers, and support.
CrossOver 11 officially supports Quicken 2009, 2010, 2011, and 2012; also QuickBooks 2003, 2001 Pro, 2002 Pro, and 2004 Pro. (I.e., they have an installer + company support; other versions may work just as well, but e.g., sans automated installation.)
You may find that you can "move up" to a more recent version by upgrading Wine to CrossOver. (Just the fact that it supports keeping each Windows app in its own "Wine Bottle" so that they can't clobber each other is worth it.)
I run MS Office on Ubuntu from a CrossOver Wine Bottle. Works very well...
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