GnuCash is a free, open-source accounting software that offers robust features for users who need detailed accounting and reporting, while Quicken is a user-friendly, subscription-based software that excels in budgeting and investment tracking but has limitations for non-Windows users. Both software cater to different user needs, with GnuCash being more suited for those requiring complex accounting functionalities and Quicken for those seeking ease of use and financial planning tools.