I have recently started to play with Panography, which is a style of stitching pictures together, however on my first couple of attempts, quite a few of the pictures that I took were distorted towards the middle of my scene; many of the objects weren't correctly aligned. Is there any way to remove any way to remove this distortion that before I take the picture?
It's hard to give a specific answer without knowing more about your post process workflow, but here are a few things you can try:
Tripod to improve alignment of objects, or - even better - a tripod with a panoramic head.
Shooting and a narrower field of view (shooting at 30mm instead of 17mm for example), this may help reduce lens distortion, though at the expense of having to take more images to cover the same area view.
Tilt shift lens. Expensive! But will produce the best results possible.
However, I think your best bet is to try better software. Photoshop has a panoramic feature that handles distortion, color differences, and other abnormalities quite well. If you already have Photoshop, it's under File -> Automate -> Photomerge. There are other software packages that may also do a good or better job.