i usually start with approx. 1 or 2 sides a4 written notes, generally i get ideas when i watch films, read books, play games or read other scenarios- decide which parts of the plot i've just got interested in i like.
Obviously i like the plot because it fits in with my campaign aims, or will serve as a useful diversion for my pcs.
If i need a map i find one- from dundjinni user creations, campaign cartographer, enworld- whereever, or else as a last resort draw one myself- i'm crap at drawing, i ran a fantastic 1st level d&d adventure using the maps from the original lara croft tomb raider- actually now i think about i've used quite a few maps from other bought scenarios and or game books (walkthrough guides).
Then i try to think of it as a story, how it will unfold for the pcs- what order things should happen in- obviously the should sometimes doesn't work out.
If it's a single session then i go for 3 to 5 encounters (d&d 4e), if it's something longer then, well it depends on how complex the plot is.
Write out what i want the pcs to get up to on a sheet of a4- single sentence for each, e.g.
Guys meet up with so-and-so in wherever, it seems there's a problem- figure patron from the list of npcs the pcs know or intro someone new (dependent on plot)
usually the intro leaves the pcs with a couple of things to check out- leg-work investigating, going to rough up someone for info whatever.
Keep writing down the next thing that happens, then the next till the plot is done.
Number the points- then draw lots of arrows- a potential flow chart.
Note i always try and get a twist in the plot, like the patron is the real bad guy, or else the thing the pcs are looking for turns out to be something quite different from what they expected- i remember an rpga scenario called something like the radiant vessel of thesk, the radiant vessel turned out to be a pregnant woman with innate healing powers- nice twist for a bunch of treasure hunting, beer-drinking, goblin-slaying... You get the idea.
Regardless somewhere in the plot something is not right-
like when my players investigated a forge making dwarforged (robot dwarves essentially), the cult behind the forge were trying to create the ultimate terminator (pass as a dwarf) dwarforged- the pcs were out to stop this happening and were lead by a brave (and violent) dwarf who turned out to be (maybe) the ultimate terminator (pass as a dwarf) dwarforged- which came as a surprise for the guy who was playing the dwarf.
The next bit is the best bit (for me) decide on the bad guy (sometimes this has already happened in my head- because of the campaign aims, or because the guy/monster in what ever media i've stolen the idea from is just obvious)
so you've a list of plot points- which of these are combat encounters, which of these are skill challenges, which of these a puzzles/traps or other.
Get another piece of a4 paper, number as above and make notes for the encounters (usually only a sentence or two again, sometimes just a heading like 'the back alley gang')- decide what you want, easy fight- easy skill challenge- hard fight- puzzle- end of level bad guy. Remember rising tension it gets harder as the pcs go on. I sometimes go for an ongoing skill challenge which takes as long as the adventurers need to figure it all out- failure just means more red herrings or tougher opponents et al.
Hit the books- generally i photocopy monsters/traps etc and put them all in a clear plastice wallets- and then into a file in the order they appear.
Lastly go back to the map and figure what bits i'm using find appropriate floorplans that will do the trick or when i used maptools just get the pictures set up and ready to play. When i was using maptools i would then have to populate every map, sort out all the monsters, maybe type up various info points, intro sections, skill challenge results etc. Playing around the table i don't do this, generally the scenario gets a life of its own at some point and i end up thinking about it much too much- so i know it off by heart.
So for a multi-level spanning scenario i end up with a thick a4 file with 40-60 pages (95% photocopied, scanned or printed from pdfs). For a four encounter one-shot i have much much thinner file with 10-15 pages in it (again 95% photocopied etc.).
To be honest these days i don't do this that often (actually hardly at all), time constraints mean i have to settle for bought scenarios.