In my current heavily modded game, I have reached lvl29 and besides a frequent ancestral ghost problem, my game have been stable... until now:

Suddenly the game crashes everytime I enter an interior cell, usually instantly, but in some instances only after around 10sec. But it does crash everytime, so I'm stuck.

I don't know what have created this, since I saw no indication, that I had done anything unfortunate until the crash happened, so I have no idea what caused it. It happened just after completing the skaal test with the stones, but I haven't done anything modrelated for the last few gamedays. But besides that I have recently played the black mill, Oluhan and then Uvirith's legacy seems to have a lot of scripts which sometimes does something. But I don't know if any of these mods are known to cause problems.

Since the crash occour in all interiors, it do not seem related to a specific cell, so my own guess is that it is caused by a bad script (like to old 24hour bug in TU2), but how can I check it? can I use the console to see which scripts are running any maybe stop some of them to see if it stops the crashes.

So it would be really helpful if someone could tell me, how to see which scripts are running in MW?

Personally, I find it easiest to look in the savegame to see which scripts are running.
Running Global scripts have a SCPT record with an RNAM sub-record.
In an interior cell, all the local scripts run for objects in that cell that have scripts attached to them. These will be in the CELL.SCRI sub-records in your Savegame.

But, it may not be a script. Some records refer to other objects and sometimes Morrowind crashes when it expects to find the referred to object and it isn't there.

Reproducable crashes are the best kind. It means that if you spend some time, you will find the object or script that is causing the problem and be able to fix your savegame.

There are 2 good ways to look inside a savegame. Enchanted Editor is used by many, but I've never used it so I can't help with that.

You can also use my http://code.google.com/p/mlox/wiki/Tes3cmd program to dump a savegame to text, so you can read it. I can help you with that, if you want.