There are a few issues raised by the new smilies. Having no familiarity with guts of vBulletin, I have no idea whether they are more trouble to deal with than they are worth.
First, as it stands, thousands of posts will have unprocessed smiley tags as many smiley names are not duplicated in the new set. Casual readers of PF who are not familiar with vBulletin and even some PF habitués who have never taken time to learn the formatting system may find these confusing. This is probably the most relevant issue for the actual scientific parts of the site.
Second, in some contexts, the smilies are a significant reflection of the communicative intent of the author. My experience is that this is especially true in the politics forum, which is the arena where smilies most often function as snark modulation operators. Unprocessed smiley tags in these situations can distort the meaning of posts for those unfamiliar with the original images, especially for those smilies with ambiguous names, or those whose appearance carries a different range of connotations than the word that names them.
Also, in my opinion, new smiley images are never simply replacements for old ones. A different image has a different visual impact and connotation. In the context of electronic communications, where smilies have taken on the role of auxiliary language tokens, replacing an image is a bit like changing a word in a sentence with a word with the same base meaning from a different language, and runs the same risk of adding or subtracting meaning.
I hope all of this doesn't end up just sounding pompous and arcane; I do realize that most people probably treat the writing of posts from an entirely instrumental standpoint, and that these issues may seem trivial. However, I would still like to make a plea for archival integrity: that from a standpoint that takes writing as including all the tools of symbolic communication in a given medium, it matters that the original images accompanying so many posts have been changed or stripped.
None of this is to say that a new set of smilies would be a bad thing if they could be attached only to new posts (languages evolve, after all), but the meanings of the current generation of posts were generated with the previous set of images, and in my opinion, those images should remain attached.
I do however concur with the previous comments that this replacement set of images does not seem particularly good. In terms of the available meanings, the important slots covered by 'rolleyes' and 'tongue2' in the old set are absent. (And the 'tongue' image in this new set is just terrible, I mean really: [edit: new smiley image no longer available - yay!] -- it looks a guy with a triangle pasted on his cheek...) I would also avoid explicit Microsoft icons like [MSN butterfly, which isn't working], if for no other reason than that it will prevent posts complaining about them from taking up bandwidth...
Oh, and several of the smilies aren't working, e.g. there are a few different ones called 'messengerN' (for various N), but only one of them works. This appears to be because the working smiley does not require the trailing colon, so all smiley names starting with 'messenger' result in the same sequence being read.