This question is really more specific to Mint.com since I do all of my personal account management there. In the Budgets tab, I always have the unaccounted transactions at the bottom of the page where my Savings transactions sit.
For a time, I would set these as a debit from my checking account and add them into the budget accordingly. However, that's not exactly an accurate portrayal of these transactions as "expenses" is it? Not to mention, my savings accounts are also on mint, so I have the credit transactions appearing too.