well.. the k-on group pic is a scan so its done by either a pro-illustrator for the magazine or someone from the animation company, which is why its exactly like a 'screencap' and yes, i think SAI is prob the best program to use if you want to get that effect.
Well, Yukiko Horiguchi is an animator and animation director for KyoAni, and the person behind a lot of the official pictures (which includes that one), so it's pretty obvious why it looks like it's straight out of the anime.
Almost all of these artists tend to use soft, crayon-like brushes for the strokes (which are almost always black and rarely vary in thickness), and the coloring is pretty straightforward. It's not a precision job - they get away with lines crossing and objects being kinda wobbly and imperfect, like the teacups or the pearls on Yui's hair decoration. The real challenge lies in getting the anatomy close to the original.
That's easy. You can do that in anything from GIMP, Sai to photoshop, just depends on you and your skill. Aside from just cell shading though, you need to have a good understanding of colour theory / anatomy/ form etc. Generally speaking anime consists of 3 colours on a figure, but never less than 2 shades obviously. You have the base colour of the object, the shadow and then the highlight if any light is hitting it or if it reflects light etc. Though I've seen up to 2 or 3 more shadow colours in some for added depth/ intensity etc. Depending on the style you want either very thin and bold lines or sometimes the lines can increase in thickness around curves or closer objects are drawn thicker/darker for perspective. Example: [link] I made the girl and environment closest to the viewer darker and the mountains and clouds in the distance fainter. Takes a bit of practice but it's nothing impossible. Good luck!