I tried to remain as fair and impartial as possible in formulating a list of the best twenty anime in the seven years that have passed thus far, which wasn't quite an easy feat given the field. Nos. 2 through 5 were all strong contenders for No. 1, constantly being switched out of the spot during the formulation period. It wasn't until towards the very end that I remembered Spirited Away. Though the others were all more than worthy, it seemed perfectly well that the movie was most deserving at the top, given its praise, awards, and production values. After some thinking and multiple considerations, forming the list started to feel more natural once I gathered twenty titles together. I had a good idea then of which would occupy Nos. 20 through No. 16, which, more coincidentally than intentionally, contained shows that had a greater amount of praise on one side than the other (i.e. more attention from critics than from fans, vise versa). No. 15 to No. 11 featured (once again, more coincidentally than intentionally) shows that have experienced a mixture of both, as well as good deal of success, though they had not had the sort of impact, including in terms of success and praise, as those in the Top Ten. I suppose that FLCL could be an exception to the rule, but ultimately, there were other shows that there better than it in the grander scheme. The aforementioned Nos. 10 through No. 1 turned out to be the most popular shows in respect to the thoughts of critics and fans. As critical response holds a greater weight than that of the latter, there are some titles that were supported, in part, by this over some of the more fan-intensive ones (Eureka Seven over Gurren-Lagann, Millennium Actress' placement on the list comes to mind). Of course, it is overall merits that hold the greatest share in the decision, so the picks were not solely limited to being some popularity contest.
Of the twenty appearing on the list, a quarter were Madhouse productions. While they have lacked the sort of individual fame that other studios, such as GAINAX, GONZO, and Studio Ghibli, have (is it a "G" thing?), they have produced more hits than any of them combined in the last seven years, if not longer. Their recognition is beginning to grow, thanks to the successes of Death Note and the film The Girl Who Leapt Through Time (Toki wo Kakeru Shoujo) (though that has come at the expense of works after them, such as Claymore with the former, being held in comparison with the two--a common problem with new-found fame, especially for a studio that has produced plenty of good, well-known shows before). Though Ghibli has made the No. 1 anime and is one of the most prolific studios in the world, it would be difficult to overlook the work that the former has done. Even the popular, resurgent Production I.G and GAINAX (two titles on the list apiece; one of which being a co-production between the two), creating impressive anime in their own rights, haven't had the kind of success that Madhouse has had this decade. Hopefully, the studio will continue to gain the following that it so well deserves.
As many a great series that has debuted thus har since 2000, there has yet to be that one work that defines a decade or redefines the genre it was placed in--an "epoch maker", if you will. The '70s saw the establishment of certain genres (e.g. Mazinger Z and Getter Robo for giant robots; Cutie Honey for magical girls), the '80s had the Mobile Suit Gundam movies (redefining the giant robot genre) and Akira (raising the bar for theatrical works), and the '90s saw Neon Genesis Evangelion, another redefinition of the giant robot genre and perhaps of anime in general. These "epoch makers", often unique works that successfully introduce new and provocative ideas, have also influenced future works, in which those, in turn, go on to influence others. While this decade has yielded titles like FLCL, Spirited Away, Gurren-Lagann, and Fullmetal Alchemist, none have really had the sort of dramatic effect on anime or how it is presented like the ones previously mentioned have. Recent worldwide megahits The Melancholy of Haruhi Suzumiya and Death Note have ended too early to tell if that is the case as well, but there appears to be nothing to the contrary, either. Even a legend like Cowboy Bebop didn't create a revolution of change or have a host of aspirers or "copycats," so pure excellence and uniqueness is not enough to reestablish the establishment. No anime in the last seven years have had that kind of "air" about them. Some may say that about Gurren-Lagann [being a "redefiner"], but it was more of a perfectioning of the super robot (sub-)genre and the sheer absurdity and "big action" that often signifies it. The same can be said in some respect to RahXephon. Despite how many called it "superior" to Evangelion, it does not make it an "epoch maker" in its own decade, as it, more or less, perfected a (sub-)genre that was already established by the earlier series and did not do anything that would constitute it as otherwise, other than being a great production. In retrospect, however, Evangelion and Akira came out towards the end of their respected decades, so there is still the possibility that we may very well see a groundbreaking title, or two, before this time closes out. And like many of the other "epoch makers", we'll probably never see it coming...
The period from 2000 to 2007 has certainly been a blessed one for the anime fan, as we have seen a great deal of works that have been of high quality. From The Twelve Kingdoms to Fighting Spirit, and from FLCL to Spirited Away, the number of top-notch productions as chosen as part of the top twenty can easily be complemented by twice more. Though there has yet to be that one work, or works, that have defined it or their respective genre, one would be hard-pressed to deny that this decade, as it stands, has founded more than enough to make it a very enjoyable one, nonetheless.
EDIT 1 [06/07/08]: Added The Girl Who Leapt Through Time (Toki wo Kakeru Shoujo) as another title that had brought Madhouse greater fame and recognition. I would be remiss not to rightfully include it here, as it was a very notable work of theirs which, too, brought them a wider spread of attention.