My favorite courses were the methodology courses. Understanding how to research has helped me research the various genealogical sources that exist, along with taking a more methodical approach to other aspects of my life as well. The courses really broke down for me not only the how to do genealogical research, but why genealogical research should be methodical. These courses helped turn my office from a disaster area into a well organized genealogical fortress.
My favorite would be the Analysis and Skills Mentoring; you actually get to phone and chat to someone. I loved the chats I had with the mentors, wish more of the courses did this.
Although I highly enjoyed the 'United States: Census Records' course (my favorite for course content), I am pleased to report that completing the assignment 'Message Boards' in week 3 of the course 'Electronic Resources: Using the Internet,' led to a possible and promising U.S to Ireland connection that I was not previously aware of. The assignment required posting a surname query to a surname message board or forum. Granted I could have posted the query on my own, but I would not have done so at that particular time--having almost lost confidence in surname message boards due to a perceived 'needle in haystack' scenario, while having to work with a common Irish surname.
There is much work to be done yet, but I am further than I was before, and I'm so grateful I took the 'Electronic Resources' course.
So far I think my favorite courses have been the US Migration course, the Maps course, and the English courses I've taken (especially the names course, which I think would be more broadly applicable than just to English research, and the apprenticeship course). My choices are mostly for the course's written content and/or the projects. I haven't been studying for a particular certificate so far, just taking the courses that interest me.
I've signed up for the next term of Boston University's online genealogical certificate and am planning to not do much in the way of NIfGS courses while it's going on. I'm scheduled to take one NIfGS course that starts in April and then to take a break until late summer, as the other course runs from early May to early August. Perhaps others of you who take NIfGS courses might be interested in the BU one as well.
My favorite course so far is US: Land Records, but then I'm just finishing the first eight courses in the American Basic. I've always loved land records, particularly when I get to draw surveys in metes and bounds. Being able to do the maps really comes in handy when you find a partition suit.