Here's a simple method used in wargames and other gridless games where you still need precise measurement: a ruler.
Or measuring tape, actually. You can get a cheap one in a mini-sewing kit, and it's really small too.
For a burst, the caster must mark the target point. Then measure in eight directions, trying to space them out so your marks describe a neat circle. I can freehand a circle from four points, but try eight and if that's too hard just measure a few more. You can also just measure from the center to each potential target (which saves a lot of time if half the area is empty) but this can tip smart players off if you measure for a target that they don't know exists (invisible, etc).
For a cone as defined in 3.5 (a quarter-circle), the caster marks a dot in the direction where he points the cone. Then measure the cone's length such that the caster and his dot-mark are along the line. Mark the end-point. Place a piece of paper that you know has a square corner with one corner on the caster, and try to get the corner centered, and draw a line along each edge away from the caster. Remove your paper, measure along one of these lines to the length of the cone. Do the same for the other one. These are the outer corners of the cone. Still using the caster as the center, use the full cone length to measure to between the end-point and a corner-point, until you get a quarter-circle.
More simply you could just draw a circle as for bursts and have the caster choose where along the line he wants his end-point for the cone. This makes the cone more accurate for the caster. The problem is figuring out for any cone direction where his side corners are. That's why we do the piece of paper corner thing above.
If you have a grid mat with a wet- or dry-erase surface, it can help with measurement, but cones always seem to cause problems.
SRD states that any target which is in a square touched by the area of effect is affected. If you're not using a grid, I suggest that the rule applies if the area touches the base of the figure. This grants a slight benefit to figures with nonstandard bases, but halflings should be dodgy anyway.
http://www.d20srd.org/srd/magicOverview/spellDescriptions.htm#areaEDIT: I had a bad method for the cone, and anybody with a lick of geometry sense would have slapped me for it.