I've just done a quick comparison between a few finance applications, using a large QIF extract from MS Money. The fact that the majority of these applications cannot import the data correctly is quite shocking:
These are the final balances reported in each application:
BankTree: 3,062.13 - BankTree was extremely slow to import vs all the rest. It also ignores the opening amount.
GnuCash: 7,264.40 - GnuCash ignores the master line on split transactions and sums the underlying splits, ignoring any unassigned values
HomeBank: 1,070,311.31 - HomeBank completely ignores multiple transactions for the same amount on the same date!
Microsoft Money: 2,965.42
Money Manager Ex: 35,033.42 - Money Manager Ex seems to just ignore transactions without a payee specified