Best is relative - so how do you define fan site, and what elements do you want to focus on, and how much time do you have to keep it up? :)

The best fan site I have seen that is really focussed on fans participating is http://friends.mavs.com with all kinds of graphics, photos, and videos in use, the official fan page for the Dallas Mavericks NBA team. Since it is an "official" site they have an advantage in that they have also invited some of the players to participate in it to give it a celebrity feel. I have not really looked at it in detail since it was redone. It has gone through a number of changes. It looked more glitzy ,now the look is more fan focussed, and I read an article once where they were the first client for the business solutions service so the site, which is a Ning the company is at http://www.ning.com last I checked, so they had a professional tech person running it but it got very heavy with special effects and would not load well then they hired I think or have a volunteer fan keep it going. It looks like they have refocussed it and put the fans first. I know that the philosophy of Ning is that anyone can start a site about anything and they are trying to make it as easy as possible for people who have zero programming knowledge to put up a nice looking place and the fans can also customize their pages. There are templates and it can get really very attractive. I don't even know if my page is still there I have not seen it in a whille, the link is from my member page to it if you want to take a look.
(Don't tell anyone, but Mahalo has a Ning that seems not to be in use any more, they need work to keep up, probably you can search it and find it)
One problem with Nings is everyone can have one, and they seem to multiply constantly but very few of them are active, it takes a real dedication for people to use them so there are a lot of abandoned ones out there - but they tend to look attractive as the instructions create them that way, and they tend I think to be organized naturally because they are built to be organized so you dont have to do everything on them just set them up.

If you want to focus on Nings here is a very brief entry with 3 Nings this person recommends
http://beyond3rs.ning.com/forum/topics/just-what-is-a-ning?page=1&commentId=2814752:Comment:1649&x=1#2814752Comment1649

Here is my fan page on the one above, it took a lot of time to make it but took hardly any technical knowhow to do, the Ning controls are easy and the fan individual pages are really customizable there are templates plus the fan site administration can make one or more custom templates with the appropriate logos and photos that all fan members can choose to use otherwise they can use any photos they want or use photos that are in the system posted by others. http://friends.mavs.com/profile/jumper Be warned, it loads slowly, I liked all the graphics and gadgets and doodads and put too much in there, but by the way, if you scroll down to the very first entry in my BLOG, you just might recognize someone!

The best fan site that I have seen that is unofficial, that has more of a news focus where the fans can comment if they wish is this one coincidentally also related to the Dallas Mavericks - an unofficial fan site set up by a fan. It may give you ideas for setup, but unfortunately it is a free fan site that is part of a free sports fan sites network and they do take a lot of time once your audience gets active as that person had to find replacements for posting and they generally post new news each day, so they got others to post also, it took years to get an active fan base but that took a huge amount of volunteer time - it has a nice clear layout. http://www.mavsmoneyball.com from the sports fan site network here http://www.sbnation.com/

This is a nice fan site that is very simply set up and needs very little maintenance. Patrick Swayze never bothered with an official fan site, but as you probably know he has cancer and has now lived much much longer than the doctors had predicted. Patrick and his wife are writing a book and it looks like they have started an official fan website, but it was based on a long time fan site that some fans ran for years using their original format, that one was low maintenance also, and they even gave them that domain name they had registered to do it. This has everything you need. I don't know what they used but to me it looks like that could even be one of the ready made templates you can choose in Wordpress? or an out of the box web page program or some other free or low cost site that has maybe an instant step by step setup for a website and that is all you need. http://www.patrickswayze.net/

Jerry Stackhouse of the Dallas Mavericks has an official website that is basically a fan site that he maintains and it is a very attractive but simple layout. I don't have any idea what software or setup they are using but it looks really low maintenance once set up. http://www.jerrystackhouse.com/

A more up to date page that automatically updates due to the feed on it is the Jason Terry official page that he has made for his fans (doesn't it just look like he has taken components from the Ning and put them together? ) http://www.jasonterry31.com/index.html if you look in the bottom right hand corner it is a link to the person who made the page for him, I believe that is the same fan that has been moderating the official Dallas Mavericks Ning I mentioned at the top and doing a great job so you may be able to get more ideas looking at his stuff.

If you are going to need a lot of tabs for different topics or projects this one may be one of the best fan sites I have seen for that to use as a model, it is a fan site for Paul Potts the opera singer. http://www.paulpottsopera.org/

Would facebook fan pages be the answer you are looking for. Some of the greatest digerati use facebook fan pages for their fans and it seems to be the ultimate fan site. Why? Simply because it is a fan site/page where you are able to socially interact with your fans. It works. Regular fan sites are about you telling your story, but very little interaction. Fans want to be involved and social media now allows for that.