I have been experimenting with ways of keeping a journal for my research since I started my PhD. I have done everything from simple mark down files, to email reminders and a simple tumblr log. The usual trade-off applies to journaling as well either feature bloat or too simplistic to be expressive.
Integrating the journal writing into the normal workflow is the hardest part. Text files tends to be forgotten since they are not in your face but hidden away in some folder; so, a journaling habit takes discipline to hold up. Email reminders were useful but user interface most email clients and my reluctance to spending time on email made it not work for long. The tumblr log worked good for a while; the interface is nice you can view previous posts easily. In the end I lost out on tumblr too since I have to log in and start writing - it was just too easy to put off over things that are more important. In addition, it was not as expressive and easy to survey as I wanted. Therefore, I started looking around and I found Day One.
Day One is fabulous compared to most of the options out there. It supports markdown, tagging, location, and images. It has a slick but simple user interface that is easy to understand and get started with. It also has a calendar view, which makes it easy to survey if you do not write every day and it has reminders if you are not writing. It synchronizes with Dropbox or iCloud. It is customizable but not too much. The girls/guys who made it are serious geniuses. I wish it would cost more money so I could give them some.
The only thing I am missing is Latex support for some Math journaling....