So I got bored again today, and I was watching EitB...and OMG I HAD AN EPIPHANY!!
IN EitB...while B&B are talking up on the balcony. Labworld!Brennan says something that I believe is VERY revealing of how Canon!Brennan feels.
"I believe you would lie about it so I wouldn't have to carry that burden."
It was the wording there that caught my attention: BURDEN.
How I interpret this? I think that Brennan is actually QUITE aware of how Booth feels for her, and that he keeps it from her because he cares for her so much. She realizes at the end of EitB that Booth has been "waiting" for her to catch up with her feelings. By having Labworld!Brennan say that line, she acknowledges the love that she knows he has for her, while using her general faith in Booth as a jumping point to the grand revelation at the end.
Feel free to debate, expound, yadayadayada, whatevs. I just had to share my geeky analysis. :D