I'd mark up my costs for toner/paper at least 25%, if not 50%.

I had to do the same thing last year because my printer wasn't working, so I prearranged it with the publisher and took my disk (with the manuscript on it) to Office Max. They printed out the whole thing for $10.86! Sorry, I don't remember how many manuscript pages it was. In your case, I think 5 cents per page sounds fair.    

I don't charge separately for this, figuring it is a cost of doing business, but if the manuscript is especially large, I might add an extra hour of my time for being there to monitor the printer--which essentially covers the materials costs. I think to charge a page rate you'd have to be able to figure out the cost of each piece of paper (about 1 cent a page, I believe) and how many pages one cartridge will print. Don't know about the latter. My cartridges cost about $30 and print at least a ream, so that would be around 5-6 cents a page. Seems to me 7-10 cents a page is reasonable, but I'd work it out with the publisher first because they may not be used to such a charge and not willing to pay it.

If it's just on regular laser paper stock, I'd charge 10 cents a page. If it's on a high-quality nice stock that he requested for presentation purposes, I'd charge more, like 25 to 50 cents. If you did not mention this cost in your original quote, however, you might want to think twice about charging at all, for the sake of good relations. :-- )

I would not charge separately for the materials involved in printing, but would include it in my fee for time. Postage, however, I would put in as a separate expense, because it's easy to back up with a receipt if necessary.

You may want to consider going to one of the Kinko's-like copy centers around the University of Washington. Their rates are pretty competitive (about 10 cents or even less per page), and you won't have to worry about separate paper or printer-cartridge costs. I do agree that these are costs that are better left for a freelancer to absorb. However, I would charge for my time to attend to these "admin" tasks.

I think that in the future you could call out an extra charge for printing costs for projects not delivered electronically. Your professional time is definitely separate from supplies. But for now, since they weren't expecting it, consider it the cost of business. You'll just know to do it differently next time :)

This is a little tough, as you are really putting some mileage on your printer, not to mention feeding it paper and ink cartridges. I've never actually billed a printout charge, but my idea at the moment is that I'd perhaps charge my per-hour rate for the time it took to print. The kind of printer you have may make a difference, so if the per-hour total looks too low, I'd raise the rate a bit, especially if your cartridges cost a lot. I'm not sure I would break out printing/supplies separate from the editing hours, unless you had already used all possible editing hours. I did work with one client who charitably offered, given their low per-hour editing rates, to do the to-author printout for a 1,000-page book themselves from my disk.  Would your client be amenable to that, or do you want to do a fast look-through of the pages?

Was your original agreement for copyediting only? Did you know you would be printing this? Is there any way the publisher could print and mail it instead? You could mention to your contact that you hadn't allowed for the cost of paper, printing, etc. in your original estimate, and that you would like to add, say, a $15 or $20 supply fee to the overall bill to cover the extra expense. (Have a firm number before you call, and be prepared to explain it, although you probably won't need to.) They will either say yes (in which case there's no problem) or no. If they say no, and this is a publisher you work with often, you could tell your contact that you will eat the expense this time--they are good clients, you want to keep their goodwill, etc.--but you are running a business and must add a supply fee in the future if you are to do the printing. I find that publishers are very reasonable, especially if you are not confrontational, but they don't appreciate surprises, so let them know what you would like to do and why.