Personally, I blame 'Dawson's Creek' for making it the crutch it has become. While looking for examples in various transcript sites and just from basic googling, I found many instances in which the characters of Capeside resorted to the excuse of "It's complicated" to get out of splainin' their situation.
And everybody else seems to have picked it up and run it right off the field!
Here are a few examples:
"This is gonna be more complicated than we thought."
'Judging Amy' (Stupid me, I forgot to I.D. who was speaking!)
A: NO, WE HAVEN'T. YOU NEVER TOLD ME WHY YOU BROKE UP.
B: BECAUSE IT'S COMPLICATED.
A: WELL, WAS HE DRINKING? WAS HE CHEATING? WAS ANYBODY GETTING BEATEN?
A: YES, YOU NAILED IT! AND HE WAS A CROSS-DRESSING SERIAL KILLER.
Also from 'Judging Amy':
Judge Amy: HONEY, IT'S COMPLICATED.
Daughter?: YOU ALWAYS SAY THAT WHEN YOU DO SOMETHING WRONG.
D'Argo: "Wormholes... Earth... what?"
John: "Look, it's complicated."
D'Argo whispers: "I understand that."
This was from a review of an episode of 'Smallville', but obviously based on this excerpt, the line was spoken in the episode:
Clark's confusion over how to back away from that intimacy without explaining his reasons is again perfectly portrayed by Tom Welling. You can see how much it hurts Clark when he tells her, "It's complicated." You can see how much he wishes he could tell her his secret.
Also from 'Smallville"
Lois: Really? You two?
Clark: We never...
Lana: Not really.
Clark: ...had a thing.
Lana: It's complicated.
Lois: [She has heard enough.] A complicated thing. Never mind.
SEAN: Well, um... If you do, then I'm a little confused. He said you're calling things off.
ZOE: Sean, it's complicated.
Ellen: Yeah, well, I -- I, I wanna be, uh, out, an' I wanna be open but it's complicated, you know? I mean, it's just it should be my choice who I tell and then when I tell 'em.
'That 70s Show':
KITTY: This tape? HOW DO THEY GET THE MOVIE ONTO THE TAPE WHEN IT'S WAY THE HECK OVER HERE, RED?
RED: It's complicated.
'Joan of Arcadia':
Kevin: What do women want?
Kevin: What else?
Helen: It's complicated. I think you might have to spend the rest of your life figuring that one out.
Here's one from the major culprit.....
Mitch: So, uh, it's complicated and, um, actually I don't know exactly how comfortable I am talking to you about this.
'Buffy the Vampire Slayer':
Buffy: Because I have obligations. People that I'm responsible for, or to, or... (Tom laughs and so does she) with, or... It's complicated.
Garret: It's complicated. You know, truth is we disagreed about the case ten years ago. Mother's killed. Father's a suspect. There's a daughter involved. You do the math. Woody.
Angel: "I tried to do what I thought was right. It's complicated how this all happened, Buffy, you know? It's kind of a long story."
PRIOR: You do not believe in a higher power?
LANDRY: Well, it's complicated. There are a lot of different points of view about that subject around here.
Tigh- It's complicated. It would take about three weeks to explain
JESS [passionately]: What are you doing? Living at your grandparents' place? Being in the DAR? No Yale - why did you drop out of Yale?
RORY: It's complicated!
JESS: It's not! It's not complicated!
SYDNEY: I know it's complicated--
VAUGHN: We're not together anymore.
SYDNEY: Since when? ...
DEX: Then what is he doing – exactly?
SHEPPARD: It's complicated.
DEX: You can do better than that.
Actually, I can't. So I might as well call it off at this point since you get the general idea.
And if you don't... well, it's complicated....