How to keep and organize a research journal/log/diary/notebook? I have read in multiple places that it is a good practice as an academic to keep a research journal.
For example, Marie desJardins' paper How to Succeed in Graduate School: A Guide for Students and Advisors says:


  Keeping a journal of your research activities and ideas is very useful.
  Write down speculations, interesting problems, possible solutions, random ideas, references to look up, notes on papers you've read, outlines of papers to write, and interesting quotes.
  Read back through it periodically.


My first attempt was to write my ideas in a log book.
I soon gave that up because the book would not always be with me when I wanted to write something in it, and because I knew eventually I would lose it and not be able to retrieve information from it.

My current approach is to write a huge LaTeX file which I store in the cloud.
In it, I chronicle my daily thoughts about my research project, to take notes of what is discussed in meetings with my adviser.
However, I simply feel overwhelmed by the volume of writing and the amount of repetition that I find in my research journal.
I also have other files which serve similar purposes.
For example, I have a file called results.pdf where I write out all my theorems and propositions and their proofs.


What have you tried and how has a research journal been of benefit to you?
Do you do all your "rough work" in a research journal, so that you can refer to it later?
What system do you use as your research journal?
Do you log all your experimental results into a chronologically organized research notebook? (Since I am not from a biology/chemistry/experimental background, I am curious as to how people who do lots of experiments manage to organize their results and ideas.)
Be aware that only you will ultimately be able to answer this question! Each individual works differently, so take the following cum grano salis.

As you've noted, a physical notebook does not always work well. Not only it is difficult to carry and easy to lose, it is also not easily searchable. (Despite this, I personally use a series of cheap notebooks and paper folders to enhance my thinking and contain random notes during the initial stages of research.) For many researchers, electronic files are the best alternative to paper. Your LaTeX file is a good beginning, and sounds like all you really need is a way to organize the huge mass of material now contained in a single file. 

I would suggest breaking the file into several files, each containing a separate aspect of your current journal. How you organize this is ultimately up to you. Use the logic and structure that meshes with the way your brain works. Only one hard and fast rule: Never have a file labeled miscellaneous! This will end up catching all sorts of odds and ends and junk, and you will NOT be able to remember what the file actually contains.