Welcome to the group! I manage a wiki-based knowledge base at a market research company. I can't comment on implementation at R&D companies specifically, but here are a couple of steps we took that I think have helped:
1. Start with a clear vision for the overall site organization. What kinds of content do you anticipate, and how will your users expect the content to be grouped? You can create this structure in advance to start things off on a productive path. On a more micro level, think about what layout you might need for certain kinds of pages like research notes or meeting notes, and create templates that anyone can use as a starting point.
Even though flexibility and openness are part of the appeal of wikis, we felt it was better to start with this kind of structure in mind, and let people tell us where they needed more flexibility. Without this, you risk running into problems with navigability and searchability, and unwanted inconsistency between pages. Even something seemingly minor like standard page titles can go a long way to creating consistency and making the wiki easier to use over the long term. And things like page templates reduce the burden on the end user, letting them start contributing right away without having to feel their way around the technology first.
2. Think carefully about your workflows and what you can do to build them into the process. Who do you expect to contribute? Is review or approval needed from certain users for certain pages? Who needs to be notified when something is updated? Collaboration works well when everyone knows what's expected of them. Also, will someone be responsible for "curating" the wiki (re-ordering pages, updating templates, etc)? Wikis make it easy for users to contribute here and there, but the average user either doesn't have time or doesn't feel they have the authority to make broader changes - and personally, I'm not sure those kinds of tasks are a good fit for crowdsourcing anyway.
You didn't mention technology, so you might have already made that choice, but for what it's worth we use Confluence and I've been happy with it. I'll be at KM World and would be happy to talk if you'd like to hear more.
Hope this helps,