I like the Workrave very much, however I still have problems with setting the right time combinations for me.

It slowly leads me to full ignorance of any blinking windows. You know, one is forced to ignore much of ads everyday and has not problem to ignore the pesky "You need a break" message ;-)

However I know I REALLY NEED those breaks. Just cannot find the best length of uninterrupted work. Might even be, that such a value does not exist in any exact form.

You know that. I type a letter, nearly finishing it, and exactly at THAT moment Workrave is disturbing the most. The time between breaks was a little bit shorter than needed. However such situations are hard to predict by simply setting the exact times.
And maybe a minute later, I start thinking, stop using the keyboard and mouse, even the monitor. In fact, I could formally take a "rest break" and even walk away from computer.
If the program was A BIT more flexible, it could detect that I'm no longer working, and offer the pause automatically in that moment.
Because since he dosen't do that today, it's fairy possible, that next time he will offer me the timer-based break again in the time AFTER MY BREAK, when I will be working hard again with no need to be disturbed... I'm simply "out of tune" with Workrave. Very unpleasant.

So, let's imagine:
The Workrave offered me a break, I has been working, no break at the moment. The annoying blinking window finally went away (should even shut up earlier -could it be set inside of preferences?).
After a reasonably short while, I stopped working for a while. The program has detected that, and assumed that I started the break myself. It should offer me the break "formally" and since I will NOT interrupt it this time (using keyboard or mouse), I really took the break.
However if I didn't take the break either, within the set timespan, program should keep offering it the same way as it does now.

I should not need to click on the panel and "start" the break manually, because it annoys and takes the focus from the work. When I think about problems, I don't have a capacity to think about breaks. The breaks should come in the most natural, effortless and seamless way. And by the means of RSI prevention, I could relax my body while not interrupting my brain. And this is what the automatic detection of flexible breaks could offer -take the very needed break for my body, the re-gained respect for Workrave's messages, and less of feeling "repeatedly disturbed" from intelectual work. Everyone who works intelectually knows that not many things annoy so much as the moment of being disturbed from thoughs.

The feature should be "optional", one should be able to set it back to "exact" time lengths. The function should be named "flexible mode" or so.

The activity monitoring, that would go on background, should be quite "slower" for the purpose of the flexible-break detection, than it is with regular timer-based rest breaks. I'd say, that in order to the user's inactivity be considered the "spontaneous rest break", user should have stopped working for TWICE the time, that usually triggers start of break when it is offered on timer base (blinking window).

And yes, the rest breaks in this mode should NOT have cumulative nature. If user took flexible break shortly after timer-based break was offered, the time between should not count because we are trying to FIND the best time now, yes?

Of cause, the all-day activity report should be available in graphical form, with some statistics. All "successful" and "unsuccessful" rest break attemps should be listed. It would allow user to tune up his timer preferences.

The idea has more potential to grow -if some more logic was applied, for example some kinda fuzzy-fourier logic, Workrave itself could offer user the optimal times, based on gathered statistics.

I'm a bit confused by your request.

When you stop using the keyboard and mouse, workrave notices and starts a
"natural break". If one was offered "formally" at that point, you'd be
forced to start using keyboard and mouse again, (even though you were just
reading the screen at the time) or click "postpone" or "skip" (which are
disabled in my configuration)

If you feel that you are ignoring the "prelude" windows, you can ask
workrave to force the break upon you (still allowing you to "postpone" or
"skip" if you so desire)

Workrave is about interrupting your work and forcing you to do something
else for a brief period. This inevitably leads to some loss of focus. I
don't think it can be helped. It is the nature of "interrupting". 

During the course of a day, you will no doubt have many different
activities. Typing letters of different lengths, reading e-mail, surfing,
etc. This means there is no such thing as an "optimal" time, because
workrave can't know what you are currently doing or how long you intend to
keep doing so. Furthermore, I think it is important for workrave to behave as predictable as possible, such that the user always knows what is (about to be) happening.

So I am a bit unsure how your request can be implemented, short of reading
your mind.

Today my colleague took a break, so I preempted Workrave and went outside, talked with him and others. I came back to work on the computer, probably 9 minutes after leaving. To my great surprise, about 5 to 10 minutes later, Workrave asked me to take a prolonged break. I always assumed that Workrave considered "natural breaks" properly.

I was about to file a ticket, but if I understand Peter, he is requesting the same. By default, Workrave suggests a 10 minutes break every 45 minutes of work. As my "spontaneous break" must have been just short of that, what it did was simply to pause my work time counter, so instead of prompting me to take a break during my spontaneous break, it prompted me about 9 minutes later.

There is surely no perfect way to prompt for breaks, but this almost feels like a bug. It means if I take 2 6 minutes breaks during a period, Workrave will still ask me to take a 10 minutes break. This makes no sense to me. I am not a health expert, but intuition tells me that 2 breaks of x minutes are better than 1 break of 2x minutes. So 2 breaks of more than x minutes should surely avoid a 2x minutes break.

I think this can be solved quite simply. Instead of requiring a 10 minutes break each 45 minutes of work, require breaks totalizing 10 minutes each 45 minutes. This can be done by prompting when a time count reaches 10 minutes. This count would increase by 1 second for each ~5 seconds of work, and would decrease by 1 second for each 1 second of break. This count should not go under 0.