Reproducible research with the publication of a "compendium"
From Faculty1000 (sub only) I found this paper, from the people of the bioconductor project on a new way to publish results as a document where code and words are woven together to create a "compedium". The document can them be browsed and the code changed in an interactive way. The authors give a concrete example using R packages and data from Golub et al. on cancer classification by expression data analysis.
I never used R so I'm still messing around trying to install everything to try this properly but at first glance it looks like an interesting concept. This way with the publication of results you would get immediately the methods, you could change parameters to check some hypothesis, etc. It would certainly help referees to check some ideas quickly. Something like this could also be used in-house as a personal e-lab book to keep track of code, data and ideas.