Basically, Meryl was sent (along with her partner Milly) to track down the infamous Vash the Stampede and do some damage-control, since every town he's been to has filed tons of insurance claims to the company she works for. Upon finding Vash, Meryl has a hard time accepting that Vash is really.... Vash. And who could blame her? Vash can be a complete idiot at times. Anyway, Meryl slowly realizes throughout the series that Vash is a really great guy (the kind that don't exist in reality; sorry, girls!) and does everything she can to help him and/or protect him. We see her step in to defend him SEVERAL times throughout the series, which first could be passed off as a friendly type of caring. But later, when she gets all misty eyed everytime she even thinks about him, and is always talking about "following her heart" when she goes after him, it becomes pretty obvious that she has the hots for him.
The clarification I needed was in the last few episodes, when he wakes up after the "incident" with Legato (hey, I'm trying to spoil as little as possible here!). The whole episode (25) just speaks volumes for Meryl's feelings. She took care of him for ten days, she fixed his bandages, she sewed his coat, she even fixed his soup. Then, when he was being accused of being responsible for all those deaths, it was Meryl who stood up for him. It was Meryl who stood between the gun barrel and Vash. It was Meryl who convinced the people (not to mention Vash himself) that Vash was not just a killer, that he was a good person. Then later, when Vash goes to fight Knives, we see Meryl crying after he leaves and telling Milly that she couldn't bring herself to say it. Say what? I think she was speaking of confessing her love. Ok, so maybe I'm WAY off, but that's what it seemed like to me. Then, toward the end of the last episode, Meryl says something along the lines of "he couldn't leave a good woman like me behind!" That just sounded neat to me.
For Vash's part, I had mixed opinions. Up until episode 25, I honestly thought that Vash just viewed her as another person to protect. She was just an acquaintance to him. True, he risked his life to protect her on many occasions, but he did that for everyone. After episode 25, I'm sure that Vash has some sort of special feelings for her. For one thing, she had to be something really awesome in his eyes to pull him out of a depression THAT deep. Then, when he saw Meryl as Rem, I got really hopeful (afterall, he did love Rem very deeply, and based his whole belief/moral system around her). That, and the whole hugging scene was just too cute for words! Oh, and lets not forget their little conversation on the hilltop, where Meryl told Vash he could stay there in that town permanently and he said something like "Yeah, I might do that. That would be nice." What does Vash do after he fights Knives? He goes back to Meryl!
Also, it should be noted that in the manga, Vashe calls Meryl by her given name, instead of "insurance girl" as he does in the anime. This hints that he is at least a little bit more intimate with her. Vash also sometimes has visions of her face or image, sort of like the way Heero often see's visions of Relena in Gundam Wing. Does this mean anything? Well, I hope so. :D I've also seen a few more scenes in the manga that indicate Vash cares more for Meryl than just another friend. He seems genuinely bothered at one point when Meryl gets scared after seeing him do the Angel Arm thing. Could it be because he's worried she would be scared of him?
Even if there is no concrete evidence that they're a couple, I think it's highly likely and probably that they would end up together. And they make a lovely pair, don't they? They get along well, despite the comical arguments. They compliment each other. Vash needs someone in his life who is responsible and organized. And Meryl needs someone to help her loosen up and have more fun. They care about each other. They're obviously used to each other as they've spent so much time together. It just works. Plus, Meryl accepts Vash for who and what he is. She was not the least bit put off by his badly scarred body (when he seems embarrassed by it and says he doesn't like for girls to see it because they'd "run away", Meryl responds with "I wouldn't"). And she keeps going back to him, even after witnessing so many crazy things. Now that's love. :D