A good map for me usually starts with an idea - either an aesthetic theme, unique map feature, or setting - and goes from there. I start by roughly sketching in a layout on piece of lined paper (and usually do about a dozen or so before I'm happy) and then do my final layout on a piece of graph paper (I use 5 squares per inch) with one square representing 256 units. Then I start in Hammer and layout the most major features first using dev textures, slowly going into lighting and gameplay-relevant props until I get it ready for playtesting. Once I'm happy that the layout is good, I start with final textures and finer aesthetic detailing. I haven't done any maps with a 3D skybox yet, but I'd probably save that for after playtesting since they have no impact whatsoever on gameplay.
You'll find a ton of tutorials and articles on what makes a map fun to play, which is the most important aspect, but very few guides on finer detailing. For this I recomend studying offical Valve maps very closely, looking at how everything is put together (cp_gorge and ctf_2fort are my personal favorites for pure aesthetic). You'll probably find there are a ton of things about every map you never noticed before. Also pay attention to the number of non-playable areas - control rooms behind windows, spaces behind fances, under grates, big outdoor areas, etc. These are (usually) vital to good maps, as they help to reduce the feeling that you're just running around inside a multiplayer map and giving the impression of life and size to the game world.