Thank you all for chiming in! I have now taken 3 days complete rest, first two taking ibuprofen for the anti-inflammatory effect. Though being pain-free, I keep imagining a strange sensation in my knee, though at this point it might as well be me concentrating too much on it.
As to the exact diagnosis - it is most certainly an over-use issue, however not an IT-band related one. Discomfort is located along the medial edge of my right patella, although the precise localisation is rather difficult to pinpoint. Perhaps cleat position is at fault. On Wednesday I am scheduled for a bike fit at my local shop, we'll see what they say.
In any case, I will attempt a rather easy 25-km route tomorrow with just one climb. If it goes well, I have halved intensity of my rides for a couple of weeks, in the hopes that the reduced strain will help recovery without loosing too much fitness in the process.
Thanks to you all for the wonderful feedback!