First thing is first, you must be diligent when it comes to fitness. There is an argument out there as to whether or not fitness exercises even benefit or are necessary for younger players (U10 and U11). I don't necessarily agree with one side or the other, but my point is that we must each take into account the age level and ability of our teams and plan accordingly. With that said, there are many ways to tweak and modify some of the exercises below to better suit your players.
Personally, I grew up hating fitness, especially when it came time to dedicate part of practice to them. But when I played over in England and for my coach in college (who was also English) I was exposed to some great fitness exercises that were a lot of fun, as well as competitive and very beneficial (these are the types of fitness exercises that you will see many professional clubs run if you ever get a chance to watch a training session). Often, they involve relay races that incorporated agility, footwork, speed and conditioning, where players have to navigate different patterns of cones while sprinting/shuffling/hopping/rolling/etc. and they almost always incorporate a ball, whether the person in motion is running at speed with the ball at his/her feet or holding it over their head the entire time, or even throwing it back and forth between a teammate. In England and in college, my soccer coaches were incredible at being creative and coming up with great exercises that were very challenging physically.
I think it is also very important to focus on the idea of "recovery." By this I mean both making sure the players have enough time to recover during fitness, but also helping them practice the different elements of recovery, since this is an important part of the game. At times, in between bursts of fitness, my college coach would have us recover on a very, very, very slow jog, and he made us focus on our breathing which allowed us to lower our heart rate so that we trained our bodies to recover on the move (obviously very appropriate to the game of soccer). While we were recovering on the jog, we were usually in two lines and he would give us commands (like "up" to jump up or "down" to touch the ground, etc.) but he would mix them all up (so "up" actually meant down, etc.) to try to confuse us in order to force us to be extra sharp mentally while tired. If we quickly performed the action correctly when he shouted a specific command, we were okay, but if we were sloppy and slow and got it wrong, we would have to pay up with push-ups, sit-ups or what-have-you. So we were rewarded for staying mentally sharp when tired, (this also forced us to practice the important soccer concept of helping your teammates out, in this case by quickly telling each other the correct act to perform without letting anyone mess up).
Along with the mental game, a player's touch is the next thing to deteriorate when he or she becomes tired. Sometimes my coach would have us recover while juggling a ball between two people, forcing us to focus on our touch and being precise while tired. If we could keep it up for a certain amount of touches or time, we were in the clear. If not, again we would have to "pay up." The recovering activity was never physically demanding, but we had to focus every ounce of tired energy on being sharp mentally and physically. Occasionally, he would also run fitness exercises three quarters of the way through our practice/training session, and then ask/demand that we be very sharp in the final technical/tactical exercise. This emulated the last 10 minutes of a match and therefore we were training ourselves to stay sharp at the all important time when the other team is usually exhausted.
Check out http://www.insidesoccer.com/is-web/movie?id=685&pro=1 and http://www.insidesoccer.com/is-web/movie?id=684&pro=1. Both of these videos demonstrate several examples of the soccer movements and agility that we want our players to focus on during a fitness exercise. You can also be more creative with these exercises by working in the use of soccer balls (for instance the first video could be done as a relay race where the person running has to hold the ball over their head while going through the cones/ladders, then drop it for the speed dribble back to the line and then use their foot to flip it into the hands of the next person before they can go). Obviously you don't have all the equipment that this coach has, but you can find many different ways to make it work.
You can also use elements of a skills circuit to build into a relay race or any sort of fitness exercise for your team. A couple examples are http://www.insidesoccer.com/is-web/movie?id=189&pro=1,
http://www.insidesoccer.com/is-web/movie?id=502&pro=1, and http://www.insidesoccer.com/is-web/movie?id=504&pro=1. All of these can be made or incorporated into great fitness exercises, games, or even races that focus on elements of soccer.
Remember, you will have to make adjustments to make a fitness exercise appropriate for your team, but have some fun with it. In every other sport we see kids on the endline doing wind-sprints or shuttle runs. There are plenty of other ways to train our players for the specific needs of soccer, and you should find ways to train the mind along with the body.
http://www.insidesoccer.com/is-web/movie?id=691 -- Here's an example of a fitness exercise that focuses on soccer agility and short bursts of speed. Of course you can make all of your own adjustments to this exercise, for instance making it a relay race, spreading the poles or cones out over a longer distance, making each player turn after going around the final cone to receive a ball in the air and then sprint with it back to their original line before the next player goes. Feel free to be creative, push the players to an appropriate degree, and look for ways to make it soccer related.
http://www.insidesoccer.com/is-web/movie?id=709&pro=1 -- Although I'm not a huge fan of this exact circuit, it's another example of soccer related fitness. The players are going at a slow pace in the video in order to provide a demonstration, but you can obviously push the players to go at full speed. Feel free to substitute certain pieces of the circuit with ones that might be more beneficial or appropriate, whether it is a skill with the ball, and obstacle course, etc. Coaches should also be encouraged to incorporate some sort of mental aspect to some part of the circuit, making the players think and always be mentally sharp. You may always want to tweak the exercise so that it becomes a race between two teams (sometimes it is beneficial to get the competitive juices flowing).
