Using a wiki in this situation is pretty much the best you can get. Mainly for these reasons:
- It deals great with every media.
- It can be distributed to the web for colleages.
- It can be upgraded with thousands of plugins.
- It makes organization of your data easier than the other solutions.
This list could go on for ever but in the end its personal taste.
I use WordPress as a blog electronic lab notebook (ELN). I'm really happy with it. I always found wikis annoying without a crib sheet of codes in front of me. WordPress, like a wiki, is versioned- you can compare and go back to the version before you messed it all up! I have nothing against wikis, but WordPress is easier, more productive for most people (and more beautiful). Its also open source and there are a truly phenomenal number of community written plugins to help you.
Lastly, I think there is a big difference what different people want to do with an ELN. This is often forgotten. Some people are mostly interested in data logging, others assembling different media into a truly readable history of the experiment, others to share the record and have an active embedded conversation with collaborators. Think carefully what you want and play with different options. For me the test of what to adopt was whether I could get students to start using it. I couldn't with several options (wikis, Google Docs), but they took to WordPress quite easily- the thing I think did it was the ease of inserting pictures and the ease of the blog commenting system for collaborations and supervision.
I once wrote some stuff about why I chose WordPress in my blog, its not too recent, but its only got better in WordPress3.
Best of luck, Dave
This is a very complex area and the answer depends very much on what you are wanting to achieve. You mention that you work in cheminformatics. I've seen several presentations from commercial companies pushing their LIMS systems in that field where the processes that go on in the lab are modelled very well in the electronic system. If that is the case, then one of those systems will be your ideal (albeit probably expensive) solution. And it won't be open source.
If you are thinking more in terms of flexible, free-form note-taking then the Marketing spin that the commercial companies put on their ELN solution falls apart. You will have to find something more open-source and adapt it to your needs.
And then you have to consider what stuff you want to share and how widely you need to share it. Science funders are often very big on sharing, but equally big on putting an onus on you to protect and exploit any IP that may arise. Obviously these are fairly conflicting requirements. I note that you have tagged your question with "collaboration" and "open-notebook science" so I guess that you are not concerned about IP (or haven't been told that you should be).
My personal preference is to use a helpdesk/ticketing system to track individual pieces of work (virtually no two tasks that I work on are the same and none fit into the conventional sample-assay-result LIMS paradigm) and then to make public data that arises from the experimental work via a separate controlled mechanism. Our "collaboration" usage thus only operates inside of our tent, but that works for us.
For the record, we use RT from bestpractical.com (http://bestpractical.com/rt/). I have no affiliation with them, but their software is useful in our hands.
When we required a documentation system for our lab, I suggested Python Sphinx. Sphinx is mainly used for documenting Python projects but works well as a general purpose documentation system.
The source files are written in plain text using the reStructuredText syntax. It outputs HTML by default but PDF and other formats are supported.
We have been using it for over a year now and it appears sufficient for what we need - documenting lab protocols, software, scripts etc.,
As Pierre mentioned we do use free hosted public wikis (specifically Wikispaces) for lab notebooks. These are ideal for making research public quickly. However for raw data we usually use Google Spreadsheets and link to the sheets from the wiki, which is useful more in organizing links to content rather than hosting content. If you are interested in cheminformatics applications, Rich Apodaca and Andrew Lang have written a bunch of Google Apps Scripts that might be useful. For an analysis of using these script for an organic chemistry lab notebook see here.
Check sciNote, a free, cloud-based, open source and easy-to-use scientific electronic notebook: