ToME: the Tales of Maj'Eyal

I don't see the point of them. More often than not, I find myself closer to the offending monsters than I was when I first popped it--teleporting straight into a wide open room full of mages or right next to the very boss I'm trying to escape.

I can see the value in a CONTROLLED phase door rune, but the normal ones seem like suicide to me, or at the very least leaving my fate in the hands of the dice. Teleport runes seem like the better choice in 99% of situations. Can somebody explain to me why I would want to use one?

They make you "phased" for a little. Quoting the wiki here:

Afterwards you stay out of phase for y turns. In this state all new negative status effects duration is reduced by z, your defense is increased by z and all your resistances by z.

so there's that.

Overall, though, teleport runes are a better escape option... so long as you don't teleport away from an Elite mob and end up next to a boss or something.

Feel free to disagree, but Teleportation runes are for escape. They aren't the best option, 90% of the time, buy they are another option.

Phase Doors are more for repositioning. The only enemy I can think of that moving 4 tiles away from makes a difference for is Prox.
So their use comes from the damage reduction and a minimal break.

Controlled Phase Doors, of course, are superior in every way to a Phase Door. I'd say that's one of the only things you'll never hear a disagreement on. CPDs are just, in every way, more useful.