I don't know of specific adventures, but I can give you some advice for writing your own.
For instance, have you seen the chase rules for Pathfinder? An athletic rogue would really shine in a chase scene through a busy city environment, and it'd be dynamic and exciting too. (Pathfinder uses the d20 system so no conversion is necessary.)
Also, is this for a specific party, and if so, what level are they? Crucially, has the wizard made those fun physical skills irrelevant yet? Between Fly, Levitation, Feather Fall, Spider Climb, Silence, and Invisibility, it's tough.
Yet you can work around that kind of wizard. The obvious way is with anti-magic fields, but you have to be careful because that also negates your rogue's magic items which they may rely on. An area with Silence on it (using the Permenancy spell) can also work. Watch out for the party wizard trying Dispel Magic in that case. These methods can feel sort of artificial to the players, so be sure that the anti-wizard zone is there for a good reason (say, protecting an artifact known to be sought-after by spellcasters).
You can also cause the rogue's opportunity to shine to happen when you know the wizard is likely to be out of spells.
On designing specific challenges, I think your thoughts about video games are good ones (you mention Tenchu; thanks for bringing back many fond memories!). I'd maybe crib from the Prince of Persia series (especially Sands of Time; it's cheap these days). I hear the Thief series (from about a fifteen years ago, heh) is really good too. It'd probably be pretty easy to play through one of them and then translate it into adventuring material. Heck, just look on Youtube for a playthrough these days.