Ahhh, I guess that sorta makes sense (I don't know any js). No idea how I would edit the thickbox stuff. Hell, I had originally edited the thickbox-pack.js to make the Full Size link bold, and it worked, but when I went to take out the target="_blank" I added, the whole thing broke. Anytime I try to have it like I did before, nada.
I downloaded Lightbox from that site, though no idea how to get it working with nextgen. X( It shows up in the Effects section, but when I click on an image, it just loads the image itself, no lightbox.
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w00t, got it working. Had to download lightbox-2 from the WordPress extend, changed all the 'title' to 'fancytooltip' and everything is working nicely. Lightbox itself is prettier than the thickbox one. Only bummer is that there doesn't seem to be a "full size" link. :\
Thanks for the help. :D