Added Update 2.
Stucco is concrete. Concrete is brittle. Brittle materials crack. Therefore, stucco cracks. Boy, do I know stucco gets cracks. I just spent many hours sealing cracks on the outside of my house. Since a crack is also a hole, it lets in water and bugs.
Paint is very important when you have a concrete house. A number of houses built by Ryland Homes leaked during last year's storms. Much of the leakage was directly through the concrete walls due a failure of the paint system. (There were also many window and caulk problems as well.) Stucco requires primer as a sealer and an acrylic topcoat for water resistance. That is why stucco cracks are significant -- they break the paint and allow water through. People who got irate at Ryland started several websites (such as this one) to document their problems. You can see the scope of the problems via this Google search. Update 2: The Orlando Sentinel (subscription required) has a follow-up article on the response of regional builders to last year's leaks here.
Here are some items to consider when patching stucco cracks.
Use the right material - I used Kover Krack elastomeric patching material. I got it at Color Wheel for less than $3 a tube. I used a full tube when patching my house. It comes in several types: gun grade (what I used), brush grade and knife grade. Each of those comes in smooth and textured versions. The textured version has embedded vermiculite to coarsen up its appearance. The gun grade comes in standard caulk tubes and is the right amount for a homeowner who patches once or twice a year. The other grades come in larger quantities which may be too much for non-professionals. Do not use putty or caulk since they do not have the same qualities as elastomeric.
Have the right light - Search for cracks in the shade or on a cloudy day. Direct sunlight makes cracks very hard to see.
There is no such thing as a short crack - Look hard. Zigzag shapes are common if stucco is applied over block. It may be faint, but cracks frequently connect and need not follow straight lines.
Make several passes - Walk around the house several times while patching, preferably under different lighting conditions. If it has just rained, or if you wet the walls, cracks may be easier to see due to the water seeping back out of the crack. Mark them with a carpenter's pencil. Do not worry about the marks since you will be painting anyway.
Be generous but not overly so - Ensure you get the patching material into the crack or hole. Spread it wide enough to ensure good adhesion to surrounding surfaces. Do not put on so much that you radically change the texture of the wall. If you do, you almost guarantee that you will see the patch after you paint.
Technique - I started out using the material like caulk, ending up with thin lines. It took a long time. I sped up with experience. Due to delays, the tube tip hardened up and I blew the material back into my caulking gun. I ended up cutting open the side of the tube and using my fingers to apply it. Next time, I will use a short-bristled brush.
Note: I have added a Hurricane category to collect all these tidbits in one place.
Update 1: After drying for several days, I painted the Kover Krack material. I had no problems. After being on the road for several weeks, I examined my hurried paint job and determined that a second coat is really needed since coverage was not very good. This may be my fault since I was trying to put on a relatively thin coat of paint instead of gobbing it on. I will be curious to see how obvious the patched areas are after the second coat. Right now the patches or visible but not glaringly obvious.