I always read the Spike/Buffy relationship in season six as being like this:
It startes out with him loving her and her feeling drawn to him because he is the only one who can understand what she has been through and he wasn't involved in the spell and he lives in the 'dark' which she fnds oddly comforting (episode 1 - 5)
Then, as Buffy finds it increasingly difficult to engage with life she strives to find something to make her 'feel' this results in a couple of kissage incidents (episodes 6 & 7)
And kissing Spike is good - she forgets about her troubles and gets lost in a sea of sensation (that boy must really kiss well!) but she feels bad about it afterwards, she knows its wrong - she is the slayer and he is a souless vampire and he is the only thing that is tieing her to this world. And it's wrong, wrong, wrong, wrong!! But then she finds he can hit her without the chip activating and one thing leads to another and they go 'all the way' and she's mortified and ashamed and it's wrong, wrong wrong! - he is a vampire and she is the slayer.... But it was good and she fights temptation to go back for more (ie: sitting in her bed surrounded by garlic) (episodes 9 & 10)
Then she goes invisible and what fun! she is free of herself and responsability and she goes to see Spike and one thing leads to another... and then she discovers that she's going turn into tapiocca pudding if she stays invisible and she discovers that she doesn't want to die and so she does what she needs to do to stay tied to this world and one of those things includes Spike (episodes 11 & 12)
Dead Things opens with Spike and Buffy having a conversation. this crazy relationship is starting to look halfway normal. And she likes him sometimes and she trusts him - regardless of what she says to his face (she put the handcuffs on afterall) and its getting too dangerous. Her feelings for him are getting identifiable and they are getting too close to the L word. He calls her 'my girl' and she snaps - how can she be his girl - she doesn't want to love this 'thing' and she beats him to a bloody pulp. You always hurt the one you love - which she acknowledges at the end of the episode. In Older and Far Away Spike comes to her Birthday and its a bit awkward but she does say something along the lines of 'i was crazy to think you could hang out with my friends!' showing that she has been thinking, entertaining the possibility of maybe a proper relationship with ... (ep 13 & 14)
Then Reilly comes back - and he's larger than life and too good to be true and she's reminded who she is - she's the slayer, the Vampire Slayer and she can't love Spike not because she doesn't love him (i think she is in love with him by this stage, just my opinion) but she can't love him because he is a souless vampire and she is the slayer and it's wrong, wrong, wrong wrong! It is simply not an option. So she breaks up with him and calls him William. She is kind and respectful as she does it. (Ep 15)
So they've broken up. He goes to Xander and Anya's wedding with a skank to make her jealous and succeeds in his objective (that scene at the wedding between B & S, there's a lot of love there). He leaves and doesn't see the trainwreck that the wedding becomes. He runs into Buffy in the cemetary the next day and asks if she cried (you know how we girls are supposed to cry at weddings), and Buffy thinks he means did she cry because he had another bird at the wedding (go on, watch how SMG plays it. She looks sideways, like she's been caught out - it's small but it's there). You'd hardly cry over the fact you wearn't getting any special lovin' anymore (more likely get angry and frustrated) so for me, it suggests that Buffy feels love for Spike. Then in Entropy she's very unhappy about the Spike/Anya sex and says acidly that it didn't take him long to move on. These are not the actions of one who doesn't care. (ep 16, 17 & 18)
In Seeing Red Spike does the unthinkable. He breaks his own vow that he 'doesn't hurt Buffy' and both of them are disgusted, shocked and angered by his actions. I think she falls out of love with him then and there. And Rightly so. But she doesn't completely write him off. She still takes Dawn to his place once Willow starts her rampage and when she discovers that Spike has left town she can't help but ask when is he coming back (ep 19 - 22). This small crack in the door allows for them to reconcile in season 7, which is really what its all about.