Human starships are built with a modular construction for a number of obvious reasons. Primarily, because separating different system components in different parts of the ship makes a great deal of logistical sense and increases survivability. Also, because if you're one of those races who greets other cultures with something other than "You will be assimilated" or "It's a good day to die!" chances are you probably care about things like ionizing radiation and low-frequency vibration discomforting your crew. So it's best to keep your crew quarters in a seperate module as far away from the engines and power systems as you can manage.
Habitation spaces are best contained in the primary hull. Starfleet has played with different configurations, and has found the spherical primary hull to be ideal for most civilian applications. Therefore, the quintessential "bare bones" of Form + Function would be something that looks like the Discovery from 2001: a spherical module containing crew quarters, shuttle bays, navigational deflector and the bridge. Attach this--with a long neck for seperation--to a drive section that contains the warp core and impulse engines. Attach other parts as necessary (you'll notice that Klingons, ever the utilitarians, generally DO design their ships around this basic pattern).
Things get tricky when you add more functions to the ship and form. A sphere is ideal in terms of volume and strength to weight ratio, but for the same mathematical reasons it's a nightmare for damage control. In space, especially in combat, you want your ship to have as much external surface area as possible for it mass, thus allowing your damage control scheme to isolate hull breaches or fires before they can result in a catastrophic failure. So a photon torpedo exploding against an unshielded spherical module would blow out one whole compartment and compromise the integrity of all seventeen adjacent compartments. A photon torpedo striking an unshielded DISK, however, would blow out one compartment and compromise the integrity of the eight adjacent compartments, and even in the worst case scenario the torpedo will blow right through the saucer and back out into space instead of delivering most of its energy even deeper into the ship.
A saucer-shaped engineering module may also be feasible, assuming one places vital components directly in the center of the disk with support equipment around the periphery (much the same reason the bridge is on the top and center of the saucer, where it is unlikely to be affected by damage to the primary hull). If warp core ejection is going to be a major requirement, then the warp core itself is going to need its own little blister area just like the bridge. So in this bare-bones scheme, you have a primary and secondary hull, both saucer shaped, stacked on top of each other like the old-style Cylon base stars: bridge on of the upper saucer, warp core on the bottom of the lower saucer.
Then there's engine placement. Ideally, you want as little space between the warp core and the nacelles as possible, so the best place for the nacelles is directly below the secondary hull, probably perpendicular to it. This ship can have anywhere between two and four nacelles; I would recommend three, with two-engine capability in case one of the nacelles fails for some reason. This gives you a tripod nacelle configuration beneath a pair of stacked saucer hulls, and top it all off with a trio of impulse engines mounted between the tripod legs, maintaining clearance for the warp core ejection sequence. The deck layout fives a "feet aft" orientation so that artificial gravity pulls everyone "down" towards the warp engines while the bridge is on the "top" of the ship. The obvious advantage of this is, of course, that artificial gravity can be provided by virtue of the ship's own acceleration, allowing the gravity generators and inertial dampeners to operate in a low-energy mode, saving power. Placement of the navigational deflector will be problematic for this ship, but the best solution is to mount three deflectors on the front of the nacelles themselves and configuring them to double as bussard collectors.
As you have no doubt guessed, this would be one butt-ugly starship. But it has certain advantages, not the least of which is modularity; you can stack more saucer modules between the primary and secondary hull to use the ship as a freighter or an evacuation transport. Weapons wouldn't really be a problem either, since phaser banks could be mounted anywhere on the primary and secondary hulls and photon torpedoes could be either waist-mounted on the secondary hull or rim-mounted in turret launchers like DS9's sail launchers. Since a ship with this configuration isn't likely to be very maneuverable--though it could well be EXTREMELY fast--it's probably optimized for a kind of ultra-long range mission, like, say, retracing Voyager's footsteps in a thorough exploration of the regions Admiral Janeway passed through.
Trust me, you did!
