I'm currently using a nicer microphone (Studio Project C1, a large diaphragm condenser mic) as my main microphone on my PC. It's running through an M-Audio FireWire Solo. I use it for gaming, skype, etc. Will having the phantom power on 24/7 wear the mic out faster, or have any other negative effects? Should I be turning the phatom power off when I'm not using the mic?
In my opinion, your audio card would wear out first, being the most complicated piece of equipment which also continually produces the 48V voltage. Secondly, the FET inside the microphone would wear out, and the mic capsule for last.
It seems to me that the capsule in this mic is quite sturdy, as it can withstand 131dB!
In other words: the microphone should be considered "in use" whenever the phantom power is turned on. Being electrically active, it will tend to break over time :-)
I would advice you to turn off any unused equipment, at least for the night, every day. It not only will wear out your various electronic components, but it's also anti-economical and unfriendly towards the environment.
I agree with @sklivvz on the environmental angle, but from stories ive heard in studios over the years, they would leave equipment ON all the time. It was a given for them that equipment usually breaks when getting its first burst of power, and thats true to a certain extent, probably more for mixing desks which was what this case was based on, but I wouldnt recommend leaving it on all the time anyway, at least until someone figures out an infinite source of energy that we dont have to kill each other over :)