If you're having problems with MediaMonkey not recognizing your iPhone or iPod Touch, check what version of iTunes you're using. Version 8.1.1, introduced April 2009, makes several changes regarding VoiceOver and syncing with iPhone or iPod touch, and _some_ users have reported that after installing 8.1.1 their devices are no longer recognized by MediaMonkey.
If you experience this problem, you can resolve it as follows:
1) Uninstall iTunes, Apple Mobile Device support, and Apple software update from the control panel.
2) Install an older version of iTunes. 220.127.116.11 is the last version before the functionality was broken with MM. You can find it here.
p.s. thanks to nohitter for figuring this one out.