It used to make sense to paste data into a lab notebook. Western blots were exposed on film, DNA gel images were printed off, acrylamide gels were dried, and protocols were written by hand. However, with the increase in electronic data, lab notebooks are beginning to look like a cut-and-paste art project, with digital data printed out and taped into a physical notebook, and little (if any!) hand-written information.
Many PIs are hesitant to allow an electronic notebook, because they believe it will lead to a loss of information. I, on the other hand, think that an eLab notebook allows you to store information in a more accessible and searchable way, as long as it is done in an organized manner. However, organization is important whether your lab notebook is digital or physical, as future generations in the lab will need to access information from it when you are not around.
The key is a well-organized file structure
There are many ways to organize your files, but having a bunch of documents on the Desktop of your computer is not one of them! Choose a filing and naming system and stick to it. For example, you can organize your data into folders similarly to how you would normally organize your notebooks—by experiment, by date, or by project. Then name all files with a date (Year.Month.Date if you want it to sort chronologically), and make a table of contents at the top of the folder (00YourTitleHere). Finally, make sure this is backed up! Both locally (I highly recommend a 500GB or higher full-computer backup system, like Time Machine on the Mac) and on your university's servers (most universities offer server space at a very reasonable price, and all labs should have as rigorous of a backup as possible).
But having organized files and folders is not the end of it. You should still use a central system to keep track of all of your files, and describe the experiments like you do in a physical notebook. Here are my favorites.
This is the easiest cross-platform system for organizing your data and other files. You can create virtual "notebooks," and make individual entries for each experiment. In fact, it even looks like a notebook, with places for headers at the top of each page. Additionally, you can link out to locally stored files for large data sets (like Excel), and import images (gels, etc) in-line. However, there is no option for writing over images, so all labeling needs to be done before the image is imported into the program. Evernote is available for Android, iOS, OSX, and Windows, so you're not limited by your operating system. Again, accessibility by your labmates and/or PI is important, so regularly export the relevant notebooks to a stable, local format (like a PDF), and consider giving your labmates and/or PI a copy of your login information.
Unfortunately, since OneNote is part of the Microsoft Office program suite, fully functional OneNote is only available for Windows; however, it is currently the closest application to a notebook with the ability to write anywhere on the page. OneNote has many of the same functionalities as Evernote – link-out to data sets, import images, etc. And, again, be sure to back up regularly (since the notebooks are stored locally unless you're using Windows Live to backup), and keep a copy of your notebooks accessible.
Regardless of the program you choose, it is likely that the physical lab notebooks we use today will soon be a thing of the past. With that in mind it is important to always follow a few principles: 1) make sure that you export regularly, both locally and on a regularly backed-up server, 2) keep a copy easily accessible for your PI and labmates, and 3) have a well-organized file structure where you store all of your raw data.