I will be the first to admit I don't know if anything I say is practical, business smart or search smart but I'll throw some thoughts out and you can filter them.
1, There is an old thread on WmW where the CEO (Marc?) mentions that a lot of big media sites block all crawlers except Google and Bing and that was a problem for Mojeek. I heard the same from the guys at the late Findx search engine. So if those doors are closed to you maybe Mojeek needs to deep spider and rank sites that Google only ranks in the long tail searches. Stuff like really good blogs, wikis and knowledge bases. Maybe white list say 10,000 good big noncommercial blogs. Not just one or two pages but deep crawl. There will be a lot of garbage posts but there also ought to be some cool stuff like software reviews, product reviews and geeky stuff. If you are blocked from the big mainstream, if you've spidered the 3rd and 4th tier sites but they are not enough why not bring in the artisans? If it looks promising expand but also play it up among the geeky communities for buzz.
2. Maybe it's just the way I search, but, Wikipedia aside, I rarely see any results from the interior pages of wikis, knowledge bases or directories. (Okay I recognize that most directories left standing are crap.) It seems to me that the good ones are nodes of expertise. I do see a lot of specialized forums in the G and B serps.
3. Related to #2. Find unique expert sites and list results from them in the sidebar for appropriate queries. Go deeper than just Wikipedia and Wikihow. Heck, Mojeek could do a publicity campaign to crowd source best expert sites on a list of topics and then weed it down to the good stuff.
4. Broaden the web savvy communities you talk to beyond search and marketing. What do they want in a general search engine?
More later.