What are you using to edit the photos? (do I remember picasa?)
In picasa there is a "rotate" or something tool where you can re-align the picture. The tool is separate from the crop tool. When you enter the tool, picasa will overlay a grid so you can align.
I am 98% positive that there is also a tool in DPP as well, I just can't remember where it is off the top of my head (at work). I think it is also separate from the crop tool. When you are fixing rotation, DPP should also throw up a grid for alignment purposes.
In Lightroom, just enter the crop tool. Here, LR will overlay 2 vertical and 2 horizontal lines through the cropped to show "rule of thirds" and you can also check alignment. To fix alignment, you just put your mouse outside the cropped area and click/drag. Once the picture starts to rotate, LR will double the number of overlaid grids for alignment purposes.
Be aware that when fixing alignment, an un-cropped photo will crop in some due to the rotation.
Hope that helps.
Also, I agree, this place is great for help.