Firstly:
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http://donjon.bin.sh/fantasy/world/
This is a fabulous entire world random hex map generator. It's all adjustable including the amount of water and ice on it (each being adjustable). You need patience with this map generator however, it takes awhile to render a new map.
Anyway, as a DM, I will generate a rough world map initially that I like. I then cut out a particular region that my NPC's will run around in initially. On this original, I place each town known via general knowledge by all the PC's I then go about making several copies of that region in a folder, scribbling on each; one where I draw all the local trade routes and roads, one where I indicate all locations of magical significance, one where I reveal where uncommon towns and or tribes are living, one that reveals the location of major resources, one that reveals faction borders etc. When I place big cities, I try to make sure they're situated near a water source as well as a source of iron for their tools and armies.
When I place unknown towns, I place them in locations of isolation if I want them to be potentially under threat.
Don't worry about being overwhelmed with all of that because I'm actually sort of waffling on. All I'm really saying is, try to be logical and chronological in creating your world and placing your cities etc. I recommend you start by generating the basic map, then one on resources, then one on towns, then borders etc.
When you see a living world, where placement of everything has a reason, naturally you will see where issues can arise, territories may clash, resources may be difficult to acquire or tribes might appear vulnerable as I mentioned. A world that then naturally generates it's own conflict can then be fun because sometimes player interaction can have positive or negative butterfly effects throughout it.
A final thing I'll mention is that a player who has a specific knowledge might gain access to a specific map, bonus information such as knowing all the trade routes could be handy.
