My forts' starting location determines my initial layout. I tend to prefer large, flat areas where I can build the Ultimate Fortress, but the last fort I started is on the side of a volcano.
For my normal layouts, I prefer an above-ground entrance. That is, I'll build ramps/staircases into a tower, which rises a few z-levels. This tower then has a retractable, long drawbridge to a second tower, which contains another staircase leading down into the ground. The second tower usually has a pillbox at the top that can cover the first, as well as fortifications and siege weaponry that can cover the nearby ground. If I'm feeling particularly paranoid, I'll surround the whole thing in walls, moats, and drawbridges, and put a lava pit underneath the entrance drawbridge. Underground, the top few levels contain farming, workshops, storage, housing, storage, and workshops (in order of increasing depth). This design has the advantage of being impervious to anything above-ground that isn't flying once you raise the bridge, and deadly even to most flying creatures.
My latest fortress (still under construction) is, as I mentioned, built into the side of a volcano. As such, I've modified my usual two-tower design to a single tower, which has the obligatory bridge-over-lava-pit leading to a perfectly flattened cliff face, where the fortress resides. One z above the entrance, fortifications carved into the face of the stone allow the marksdwarves stationed there to fire at anything on the far tower or bridge. Interestingly, the volcano has a river bisecting its dual peaks, about 10 z-levels below my fort. Thus, I've constructed a staircase down 11 levels, used the river to flood a farm down there, and dug a wide channel beneath the river to the volcano's magma pit (which is actually in the opposite spire from my entrance). I intend to use these levels to form not only my magma smelting/workshop operations, but also an indoors obsidian factory.