My first thought was to have a single note per sample wherein all growth notes, data, and analyses would be presented in chronological order. The idea was to have each note be a wholly self-contained idea. Analyses which potentially included data from multiple samples would also be independent notes. These notes would be segregated into different notebooks (e.g., Growths, Analyses, etc).
Problems with this approach were readability and Evernote's per note size limit (50 MB for premium users). Having all data in one note made it necessary to scroll through a note to find what I wanted. Regarding the size limit: few files I would want to attach are greater than this limit individually but the aggregate commonly is.
So the data relevant to a single sample must be spanned across multiple notes. How should this be done? I decided to make each note as specific as possible and use note links and hyperlinks to connect related data (I wanted to say something about relational database normalization here but I don't actually know enough about that to not get the analogy wrong). The root of this sparse structure would be the "growth note" which would describe how the sample was produced and include a list of links to relevant data and analysis notes.
For example, note "Growth A" would contain the data files produced during growth along with the PDFized handwritten notes taken with the Echo. At the top of this note would be a list of links to "XRD on Growth A", "AFM on Growth A", etc... The "XRD on Growth A" link would lead to a note that would include the XRD data files, the settings used, and plots of the results as images. If comparative analysis was done which included Growth A, links to the notes containing the analysis results would be included in a separate list.