I'll probably have a very differing view as opposed to others on here. How much should a bee removal cost? Well, it depends . . .
First of all, whatever you are going to charge, keep in mind that you are getting something out of it: a colony. Sometimes they make it, sometimes they don't, but that really is neither here nor there. You are receiving a colony. The going rate for packages is $85-110 around here, and nucs are $100-145, depending on genetics. So just by showing up, getting the bees, and leaving you are up $85-145 in value.
Equipment wise, sure you can add some of the cost of what you are going to use, but it's really yours. If you are using a $150 bee vac, a hack saw, or whatnot, you get to walk away with them, and most of the equipment you can reuse. So say that you are actually 'using' $20 worth of equipment. That means you are leaving with $65-125 in value. Next would be gas. For me I wouldn't be willing to travel longer than an hours drive, which would probably cost me an additional $30 in gas, so end value is $35-95.
The rest of it depends on the individual. If you have to take off work, you should be compensated. If you are doing it on time off, or you are unemployed, or you don't have anything going on that day, I don't think you should take that into account. I'm still a student, my time isn't worth much. So I don't add that into the mix, as long as they are being flexible in allowing me to come at my next class break, instead of being like "I need you to come ASAP", that's different.
Taking a look at the end value, if you could walk away from a job getting paid $35-95 for an hours work, would you do it? I would. How about two hours? Three? That's probably about where I would draw the line. If it's going to take a while, I would charge. But if it's just like two hours, I wouldn't. But hey, that's me.
As far as charging $400, that's really a matter of supply and demand. If you are charging $200 and your schedule is so backed up that you can't get everyone done, then upping it is fine in my book. But again, to me it depends on the person, and the job.