@Mat, yes, the commercial offerings are a bit 'fill in the box'. These boxes are based on templates in most cases and the templates are quite easy to build. These are now pretty sophisticated and slick pieces of software but they are expensive and remain quite focussed on specific science areas. They should in most cases work pretty well for synthetic chemistry but I think they start to break as you move beyond that particularly where you mix chemistry, biochemistry, and computer modelling.

There is quite a lot of material spread between here and JC's Blog and other places on possible systems to use as Notebooks and what the benefits and problems are. Michael Barton recently set up a wiki at www.opennotebookscience.org which would be a good place to aggregate some of this so as to provide a central point of guidance.

I think the broad concensus amongst the Open Notebook community is that for the general non-computer based laboratory science community is that a Wiki does a good job and both WikiSpaces and OpenWetWare have pretty good functionality. For the more computer based or computer literate there are some advantages in using code repositories such as Google Code (see Pedro Beltrao's project). We hope to be able to take the Southampton Blog Notebook towards a hosting service in the future but we're some distance from this as yet.