That first shot doesn't appear to have been taken with the Sigma lens. In fact, all the shots you linked appear to have been taken with the Canon EF-S 18-55 IS. So we are really looking at possible issues with one lens here.
Some ideas...
1. Do you have "protection" filters on your lenses? If so, take them off. Clean the lenses, too (micro fiber cloth, lens cleaning fluid and a final polishing with a lens pen are recommended).
2. Viewing a 15MP image on a computer monitor at 100% is like looking at the a four foot wide print from 18" away. Use reasonable viewing sizes. Looking at the Flickr 1600x1067 pixel size files of your shots (instead of the full size), they appear a lot sharper. The photo of the church has some chromatic aberration where the roof meets the sky, but thats no surprise (and can be fixed in post processing).
3. if not already doing so, use a matched lens hood on your lenses. It can help keep oblique light from causing "veiling flare", which reduces contrast and color saturation, can make images look washed out and soft.
The f9 aperture you used should be fine, but be aware that when using smaller apertures (f11, f16, etc.), sharpness of fine details can suffer due to diffraction. You might want to Google and read up on this.
Plus, all lenses have "optimal" apertures and, with zooms, focal lengths where they perform best. Your two "problem" images were shot at f9, one at 18mm the other at 46mm. Two of the shots you are happy with are shot at f5.6 (wide open) and 55mm. The third is at f5 and 36mm (also probably wide open). It's possible your particular lens performs better wide open than stopped down.
4. Some sharpening might be possible. But that usually should be done last, after the image has been cropped to it's final, intended size.
5. The monitor you view your images on is important. A graphics quality monitor isn't cheap, but if you are serious about your photography, can be a good investment to help maintain your sanity. If going to that extent, you also should consider calibrating your monitor and your entire workflow on your computer. That means buying a calibration device and software... and using it periodically to maintain accurate color, contrast, light levels with your computer. Forget about using a laptop... the viewing angles are too variable and we use them undear a wide variety of lighting conditions.
I also notice the two images you are concerned about appear to have been shot on overcast days, in lower contrast light. All of the earlier ones were shot on sunnier days, when light was more contrasty, and that can give the impression of greater sharpness too.
6. Have your camera sensor cleaned or do it yourself. If there is a lot of adhered dust or oils on it, those can effect overall image sharpness. Also, lenses and cameras get out of calibration over time, with use and wear and tear, so a proper checkup and some adjustments might be in order. Lenses also can have an element get decentered, usually from a bump or something. That usually effects sharpness on one side of an image more than another, though. Lenses do wear out, too.... just from regular use, focusing and zooming mechanisms inside get loose and aren't as precise. Higher quality lenses are usually more durable than inexpensive kit lenses that are comprised of a lot of plastic.
7. It might help to shoot RAW and develop your images into JPEGs (or Tiffs or whatever) in post-processing on your computer. This puts you more in control of many factors, and preserves the maximum available digital data from each shot for you to work with. All digital cameras shoot RAW files to start with.... But when you set the camera to JPEGs, it is converting the RAW files via some global settings you've made in the camera menu, and in the process throws away a lot of the data from the original capture, leaving you a lot less to work with if you want to make any adjustments later.
Both the "poor sharpness" images appear to be correctly exposed, but there can be some loss of apparent sharpness if you have to make adjustment to exposure after the fact. RAW files are more easily adjusted for exposure, color balance, etc. And more or less sharpening can be applied.
If you are going to continue shooting JPEGs, you have to be sure of your camera's settings... the Picture Profile in particular determines contrast, saturation and sharpness of the JPEG image. You also have to watch noise reduction settings, since it works by slightly blurring fine details. None of these were high ISO shots, so I doubt that noise reduction was much of a factor here.
