Many gallery images have transprancy. For example, the last four images in the gallery of https://deusex.wikia.com/wiki/Richard are transparent, and the background color of the gallery thumbnail box is gold.
However, the gold background color doesn't look too great for most images in the gallery. I think it would look much better if the background is set to a dark gray that's close to black.
On second thought, is there a specific reason why those posters have large transparent areas on the sides? Cropping those empty areas could be enough to solve the problem - at least, in the Richard article.
I think the first option could potentially be improved if the background color is not removed entirely, but set to something that is different from the page background, like a shade of gray that is either lighter or darker than the page background's gray.
Option 2 (no border) could also work, and is used by a few wikis with dark background, such as the Elder Scrolls Wiki and Bioshock Wiki. This may be the easiest and most practical option.
Regarding the empty transparency areas - I made all story item images of the same dimension (1,420 × 870) in part because I pasted all the screenshots as layers into a single image, and cropped them all to the same size all at once. Doing so has one additional benefit, which is that when placed in a table (as in the above story item page), the images are neatly aligned. Otherwise, if the images are not of the same dimension, or have different transparency margins from one another, then they would not align as well.
The same technique is also used in the Ammunition (DXMD) page, where you see that all the ammo box images line up neatly. In the ammo listing page, if you were to crop out the side transparency areas for the revolver ammo image, then that image would have to be rescaled and then centered in the table cell in order for it to be of the same height and aligned with the other ammo boxes.
However, you are right that when displayed in gallery view, it looks a bit weird if there are large transparency areas. If you crop the images, I would crop all three similar images to have identical margins.
Just wanted to jump in and point out: the new gallery styles are iffy depending on how many and how big an image is. It's set so if there's 3 or less images in a gallery, it creates really big boxes (like with the Magnum one) and will only be smaller when there's 4 or more images in it (like Richard's). Also, if there's a really small sized image (say, a 100px square) it can look really bloated as the coding tries to stretch it out to fit the box, especially when it's 3 or less images in the gallery. However, if a gallery has a lot of images (like Adam's) it works well because it'll auto-hide any past the first 8, meaning you won't have to use scrollboxes anymore for those galleries.
My suggestion would be to consider what you want the most out of it: do you want to show all the images with scrollboxes, do you have a lot of thumbnail size images, etc. Note also that by switching to the new gallery style, it negates any old gallery coding you may have (you can still customize it to a degree, you'd just have to write up new code).
Kazatel's isn't too bad actually. I haven't figured out the "ideal" min. size, but if an image is large enough, the new gallery system is ok with it (basically it takes a center part of the image in that case and uses it as a thumbnail without stretching it out). It's smaller images (like sprites) that will be problematic.