My background: I have struggled with RSI due mainly to computer-based overuse for nearly 15 years. I first developed problems when I was a software developer. When I wasn't developing software, I tended to spend a great deal of my leisure time playing games (mostly FPS games using a PC with a keyboard+mouse setup). In my case, that was a really bad idea, but it seems genetics and other factors play a role as well. Others might be able to handle what I was doing year after year with no problems, or they might heal up after their injury, fix their ergonomic situation, and be able to continue at the same pace with no further problems. I am not one of the lucky ones, so I ultimately chose to give up developing software professionally and switched to a (lower-paying but more physically active) career that mostly kept me away from a desk. That way, I could continue to use a computer after-hours without much trouble. I did lay off the FPS games, though, and made MANY ergonomic improvements.
Once you're struck with a problem, it will become pretty obvious what works and what doesn't for you, because the pain will tell you. Everybody makes different mistakes, but here are the two I believe to be most common:
1) A desk that is too high.
Put your monitor wherever it's most comfortable for you, but don't think you need to put your input devices on the same surface. Lower your keyboard as close to your lap as you can, and especially your mouse. I find that if my upper/fore arms are forming an acute angle, it makes me very prone to re-injury. An obtuse angle is not as bad, but optimally, something near a right angle seems to work best, at least for me. I won't claim that it will be the same for everyone, but I will claim that most people have their keyboard and pointing device too high.
Keyboard/mouse trays may help, but attaching one to any old desk might not lower the surface enough. When I first injured my tendons, I simply got a cardboard box and put it down near the level of my quadriceps, next to my chair. That helped immensely. As others have pointed out, improving ergonomics doesn't require expensive equipment.
2) Not varying your working position.
The latest trend seems to be standing desks. I'm sure those can help, but might open you up to new ergonomic issues. As others have stated, varying your position between standing and sitting is probably better. I've found that the best thing while I'm at home is to switch between my laptop (on my couch) and desktop, seated at my desk. If you look up "correct posture", I'm pretty sure none of the diagrams will look like me reclined on my sofa with my macbook pro on my lap, but that is one of the best improvements I've made. I now alternate between laptop/couch and my desktop computer with standard desk chair.
I also highly recommend switching between various pointing devices. For me, mice seem to be the worst. Especially heavy ones. If you have a high end mouse that lets you add the desired amount of weights to it, I suggest removing them all. If your wireless mouse uses standard removable AA batteries, use rechargeable NiMH rather than alkaline batteries to decrease the weight even more.
Trackballs seem slightly better for my tendons than mice but I could never quite get used to them, and the thumb-based ones scare me. That particular digit is more precious to me than the others. Trackpads (some of them) and touchscreens are wonderful from an ergonomic perspective if you can get used to them, though my MBP's trackpad has a button which I tend to use my thumb exclusively to depress, and now my thumb is exhibiting signs of tendon or joint problems. I am learning to alternate between using my thumb and fingers for depressing it now, and it seems to be improving.
I also use one of Apple's magic trackpads with my desktop, which is a bit clunkier and much tougher to get used to (and the Windows/bootcamp drivers are terrible compared to the OS X drivers), but it's much easier on my tendons than my mice--I still use mice for gaming since nothing else is quite as precise and quick, but I limit how much time I use them and stick to the trackpads for everything other than precision gaming.
Don't think that taking frequent breaks is a good substitute for not varying your working position or bad equipment heights. I had lots of breaks while my code was compiling or my colleagues came to talk to me, and I tended to pace around while thinking about my code. I got up from my chair frequently. It didn't save me.
[1.] tendinosis.org is the best source I've found for explaining (or at least, theorizing) why some people have more trouble than others. It's only partially due to your setup, but that's the part you can control most easily.