Does any use something like this for “starting (positive) activities” as well? I do that and it’s quite helpful, let me describe how and I’ll ask for ideas on one point.
I have some goals that I track with two Beeminder-goals: One for the time I spend (a minimal commitment, M minutes/day) and one for the daily engagement (D days/week). I use this* set up for trying out habits for some period. In the early phases of such goals, I do set a timer for M minutes when I sit down to it.
When I’m enjoying the activity, I’ll repeat the timer. I’ll be thinking “I’ll count the timers and add the data point later.” But of course, I forget the count since I’m engaged with the activity. I tried to solve this for instance, by using a scrap paper on my desk. I always ended up with too much friction.
I think a Pomodoro app with a flexible timer and some kind of tagging feature might help me. @phi do you perhaps have a suggestion for iOS? I’m also happy to consider a completely different approach to such goals, if anyone has an idea 
* Do we have a name to refer to this kind of setup? I get tired of describing it over and over again. 