In a recent project I was facing a difficult challenge of trying to sort out how Exchange 2010 handles junk/spam mail. Previous versions exposed GUI features to fine tune "spam confidence levels" (SCL) to avoid issues with false positives, or too much real junk.
In Exchange 2010 this appears to be handled mostly at the Edge server level: http://technet.microsoft.com/en-us/library/bb123559.aspx
There is one setting however in the "Organizational Configuration" which needs to be tweaked particularly if you're using a hosted spam filtering solution like many of us do today.
To change the SCL level in the organization use PowerShell:
Set-OrganizationConfig -SCLJunkThreshold n
The default is a level of 4. Valid ranges are from 0 to 9. The lower the number the more likely you'll get false positives. So if you're finding legitimate mail ending up in the Junk Mail folder with Exchange 2010, try to increase the value to something like 7 or 8.