My site isn't huge, but it does have a large number of internal links. It's an editorial site of about 4,200 pages, a few dozen of which might be termed "affiliate pages" (mostly annotated hotel listings). And it hasn't been hurt by Allegra. On the contrary: Traffic has climbed by about 25% in the last several days, and the ratio of Google referrals to Yahoo and MSN referrals has also climbed back to where it was until a couple of months ago (when the Google:Yahoo/MSN ratio began to erode slightly).
In examining my server logs, I haven't noticed any surprises; as far as I can tell, the same pages are in the top few dozen spots. My rankings for the keyphrases that I track have hardly budged, and most of my neighbors in the SERPs are the same ones that I usually see. I assume that much of the additional Google traffic is coming from upward "ranking creep" on hundreds or even thousands of minor searches.
The one slight oddity that I've noticed in the SERPs is the displacement of my #1 ranking for "[ship name] photos" by a self-described "personal site" that I'd never heard of. The page that knocked my [ship name] photo gallery to #2 for that keyphrase is a directory page consisting of unannotated links. The directory page's PR is 2, the personal site's home page has a PR of only 3 and an Alexa traffic ranking of 206,378. The entire site, which came out of nowhere, consists of virtually nothing but unannotated links, which makes me wonder if outbound links are now a scoring factor. (FWIW, I have plenty of outbound links myself, so maybe that's helping me in Allegra.)