During a long expedition, how to safely pack, place and carry a portable gas filled stove? It looks something like this: http://www.climbing.com/gear/multifuel-stoves/
When packing/carrying the stove there are two main aims: to not break it and not get the rest of your kit covered in fuel. There are some tips for achieving this:
pack the stove somewhere secure where it won't get too knocked about/crushed/bent. Most stoves will pack inside a pot/pan which is my preferred way of doing this.
Similarly for the fuel bottle make sure it is well packed and try not to drop it. Be particularly aware of anything sharp. While they are fairly tough it would be very bad if you pierce it. For liquid fuel (petrol/white gas) I generally just put the bottle in a side pocket of my backpack. Also if you have a fuel bottle make sure you attach the cap securely when not in use as you don't want leaking fuel in your pack.
If you are going for a long trip bring a repair kit with the necessary spares and know how to do simple repairs on your stove as necessary. What this actually involves will depend on what stove you have. For example on the MSR whisperlite there are several o-rings in the pump which can be replaced and the jet may need cleaning.
In fact you should probably give your stove a check/service before going on the hike. This will reduce the need for doing repairs in the field.
When setting up the stove make sure you set it somewhere stable on level ground as you don't want it to tip over.
Bring sufficient fuel. Make sure you know how quickly your stove uses fuel and probably bring a bit extra just in case.
You should define whether you are asking about white gas stoves or isobutain (canister) stoves.
For most backpackers, your main decision will be between the 2 broad stove categories: canister fuel vs. liquid fuel. You may also want to consider one of the growing number of alternative-fuel options now available..
A good resource to get started if you have not yet picked a stove, might be REI here:
Typically you will want to make sure you are aware of altitude considerations as sealed bottles of white gas, for example, are known to burp, even burst and get gas all over your gear. I would say other than that, provided you are not hiking through a fire or smoking you would be safe. I carry ultra light stoves, a MSR Pocket Rocket these days, which comes in a neat and tidy carrying case to protect the stove, as well as my gear from ripping on its jagged edges.