You shouldn't have trouble with most peripherals, certainly not stuff like mice, keyboards and displays.
I use the cheapest generic 22" display I could find with my Mac Pro, because I use my machine exclusively for music, so as long as I can see what I'm doing it doesn't matter. Actually, the display looks great to me, but I'm no graphics pro!
There are no drivers for my display, so any USB control functions don't work, but I just adjust the brightness and so on manually with the controls on the display itself. This doesn't bother me at all, but if it bothers you, you would have to look for a display with Mac drivers I guess.
I use a Logitech mouse, because I don't like the Mighty Mouse that came with the Mac Pro. The Magic Mouse was released a few months after I bought my Mac, I might have gone for that if it had been available to order with my machine, but my Logitech one is fine.
Personally, I love the wired keyboard that comes with the Mac Pro as the default option, but if your preferred one is wired, it will work fine (not sure about bluetooth ones, do they need a driver?). The only thing is that a lot of the keys on the Mac keyboard are labelled specifically for OS X functions. I think using a Windows style keyboard with the Mac would annoy me, but I know some people do.
The mouse should be fine as well, but if it has lots of buttons and you use them all, you might need to see if there's a driver. I think up to four buttons probably wouldn't need a driver (as long as it's wired), as that is what the Mighty Mouse has, but my Logitech one for example has a fifth button, and OS X didn't respond to that, until I installed the driver.
You will be able to add a USB 3 card to a Mac Pro, no worries. That's one of the benefits of choosing a Mac Pro over an iMac. They're not as expandable as a PC tower, because Apple still controls a lot of things, but it does mean you can add cards to keep up with the latest interface technology without having to buy a new computer for quite a while. The reason I chose a Mac Pro is because I wanted the internal drive bays.
Macs have become much more standardised over the last decade in terms of peripherals and architecture, so you shouldn't have too many problems.
It's not quite the same story when you start looking at things like Graphics cards, but the bread and butter stuff is pretty straightforward, I think.
I'm not sure about bluetooth mice and keyboards though, not sure if they need drivers or just work.