Q:

Who was Daenerys referring to in this line?

I have been sold like a brood mare, I've been chained and betrayed, raped and defiled, do you know what kept me standing though all those years in exile? Faith...in myself.

Most certainly, she referred to Khal Drogo. The show clearly portrayed how Daenerys Targaryen became a stuff for sale  and a significant instrument of way to the goals of Viserys. Even after their marriage, it wasn't her decision and desire to be in the same room with the Khal.
Afterwards, Daenerys and Drogo found theirselves falling in love and getting serious affections with each other. Thus, it started the well-known relationship they had until Drogo has reached his death.
When Jon Snow and Daenerys met in Dragonstone to prime an alliance, she said those lines quoted at the first part of this thread's body. Why did Daenerys consider their relationship as raped and defiled? For all I know, she has been affected of how much she loved the Khal. Wouldn't that be deemed as a disrespectful approach to her heart's desires and to her husband?

A:

She was referring to Khal Drogo
Yes, she grew to love him as their relationship progressed but that doesn’t change what he did to her initially. He abused and used her for his purposes initially and that involved rape. Emilia Clarke gives some of her own insight into this.

GLAMOUR: Another criticism that's been pointed at the show concerns its depictions of rape. Khaleesi—
EC: —was raped in season one.
GLAMOUR: By her husband. A lot of people came away from that arc with the unsettling impression that almost immediately after the rape she falls in love with and dedicates herself to her rapist.
EC: Yes. Well, Daenerys and Khal Drogo's arranged marriage, and the customary rape that followed—ask George R.R. Martin why he did that, 'cause that's on him. But I thought the consensual sex she has thereafter was genius. She is physically saying, "You can't rape me again. I'm going to be in control and show you something you've never seen before." At the heart of it, we're telling a story; you need that part of the story to feel empathy for Daenerys. You see her attacked by her brother, raped by her husband, and then going, "F--k all of you, I'm gonna rule the world." That's where we are now.
Glamour, Game of Thrones' Emilia Clarke on Her Inner Khaleesi: "I Know I'm Gonna Put the F--king Wig on...and Let Her Refulfill Me"

However, given the context of the quote she is likely also talking about her brother, Viserys. Note how he used her as goods, selling her to Khal Drogo to get his army. We also see that he defiles her, the very first we see of him is acting inappropriately towards her.
NSFW Warning for the video.

The other references she mentions refers to Illyrio, Jorah, Pyat Pree and likely some others.

