Yes, this is called Selective Sync in Dropbox.
You can exclude specific folders being synced with DropBox.
In Windows 7 and Dropbox 3.1.265, you can:
- click on Dropbox system tray icon
- click on gear icon and select Preferences
- click Account
- click Selective Sync
- Untick the folder you no longer wish to sync with Dropbox
- Click OK
Be warned that Dropbox will delete that folder, so make sure to copy everything to another place before you do this and copy it back afterwards. (Thiago Duarte)