Excellent post Elias, I think you've put together a good webmaster guide and you've touched almost about everything I am doing/considering as a webmaster.
1. I'd like to add that you also need to follow the "standards", don't be too unique when layout is concerned, be generally consistent in the navigational structure with other websites. This helps the ease of navigation, as the visitor does not have to become accustomed to your website first before he can navigate it without thinking too much. Unless of course it's unique layout is coupled so closely with your design, and that experience is the value you offer instead of content. However, generally those kind of sites don't last very long. Most important, be consistent throughout your own pages! Open door maybe, but I still see many websites that struggle with this.
2. I'd put your number 3 here, because it's so much easier to get links when you have something to offer and you don't have to ask anymore, they'll start asking you, or better yet start linking you.
3. Yes, well that's the basically the question of this topic. Any thoughts on that? Regarding your example, what makes it unique is not so much it's focus on news and forum, but that it's in greek and has a offline magazine. But I get your point on capitalize on the unique feature. But that does become a bit more difficult when you have multiple features that you feel are unique, or the uniqueness lies in the combination of non-unique features. Or maybe you're not unique then.
4. You're spot on, but it's easier said than done.
5. I've thought about this, but there are a lot of "but"s and "if"s about this. When do you know you can't beat them? Sometimes the only way of joining is by giving up your built up 'establishment' and intellectual property (I can't beat Wikipedia, so I should join them? you'll be all in tears). Plus there's the fear of losing autonomy and control. There's also some conditions for a successful collaboration, which sometimes (due to the nature of the virtual world for one) are hard to predict: interdependence, commitment, trust, communication, conflict resolution, compatible values and believes. Having said that, I've got some great partnerships with some people/websites, and that works well. There's also room for collaborative attempts at making it more of a network of sites, or collaborative projects supported by the different webmasters. But a real merger won't work I think.
Reputation? You mean that 4/5 stars, and 19th place on Avitop? Well, I'm glad you're here, but I don't how much it says about reputation...?