I'm a Nikon D90 owner and I bought my camera with a typical kit that very much available in my country. D90 body, an 18-55mm VR plus a 55-200mm VR and a nifty fifty (50mm f/1.8 non AFS version). I added a battery grip and Flash to it later.
When first time I joined here, every photo I uploaded were rejected. I wrote another blog about how I learned to use the gear properly - you can check it out here - What Dreamstime Thought Me
I discovered what the sweet spots are. And also learned the sweet spots of the lenses I own. Higher aperture values, just like the lower ones may cause sharpness issues especially on the cheaper glasses but even the pro level glasses can suffer from diffraction affect if you use them on aperture like F32. All the lenses get softer when lower values but also get softer on higher values too.
I managed to take really sharp and clean photos with Nikon 50mm F/1.8 with aperture value of F/7.1 -- This is its sweet spot. And takes sharp and nice photos in every circumstance.
On my 18-55VR which is a full plastic lens. 24mm and F/8 gives the best result. At 18mm it is less sharp especially on the corners. I never use it higher than F/8 aperture value to avoid diffraction. I always try to use it with VR off, when its necessary on tripod. Because VR on the lenses also cause noise & grain when there's not enough light.
The 55-200mm VR is a puzzler. I'm using it VR off as much as I can. And using it F/8 value too but that aperture value is giving sharp results on 55mm and 70mm. I realized when you zoom more and keep the value at F/8 image gets softer. I discovered that while looking at a tack sharp photo with 70-300VR Nikkor at almost 300mm (270mm if I remember correctly) with aperture value of F/13... Now that's not suppose to happen. But when I tried the same with 55-200VR with 200mm and F/13 aperture I noticed maybe image it a bit darker but also a lot sharper.
Besides all that the options like Long Exposure Noise Reduction and High ISO Noise Reduction are disabled on the body (D90) -- these causes soft results and looses a lot of sharpness of the image.
These are my experiences and results so far. Friends who had similar or same equipment I appreciate if share your experiences on your comments.