Rei is still surprised.
Her stiff expression slowly changes into a smile.
Trajan: This shot makes me smile.
BiQ: And never again could Gainax or Khara top or even reach again this very first rendition of this ultimate heartwarming.
Leighton: My eyes watered at this scene - I actually felt happy at Rei's first expression of joy (in Shinji's presence) as a result of Shinji's care for her.
Rei: "... So he just wants me to smile? If that's what it takes for someone to get a nap around here then fine, I'll comply... but there had better be a good bed and breakfast deal in it."
Kendrix: Congratulations, Shinji! You have been welcomed into the small circle of people who are allowed to see that smile.
The 'blush lines' (The Rebuild and death and Rebirth renderings of that scene make it more obvious that this was meant to be a blush) indicate that this smile is genuine, i.e, she's not doing it just because he told her to, but mainly because the afore mentioned realization.
Needless to say, this is the point where they fall in love. This is, like many other things, emphasized in Rebuild, where they go as far as, for all intents and purposes, holding hands.
thewayneiac: Of course we'll have to see the two remaining installments to know for certain, but I agree they are in love in Rebuild. But if you are saying that they fall in love at this point in the series you are probably overstating it, at least on Shinji's part.
Kendrix: I'm not sure of that - And even if it was to early to call it full-blown love (I do not claim to be above the effects of shipping goggles), at least the romantic-ish feelings/beginning teenager crush must've started in this instant, because... when else? Anno did not have many ideas as to what to do with Rei in the action arc, (see the Anno quote someone else posted earlier), when that plot thread finally gets picked up again in the dummy plug arc, the warm fuzzy feelings were pretty much already there, in suffient quantities for Rei to show visible nervousness/embarassment in reaction to what she thought to be a compliment...
thewayneiac: I'm not arguing that Rei wasn't in love with Shinji; I'm arguing that Shinji was never in love with Rei. This is, however, the point where they would have fallen in love in a normal show.
Kendrix: I thought about the possibily of R/S being unrequited after someone mentioned it in a thread, and while I think that Shinji did show signs of attraction, I'm aware that most of these aren't exactly unambiguous, I can tell where the people who say they're just friends are coming from, but the fact that he counts her among the 3 women he's attracted to in ep 20 and bits of 26' put any doubts aside.
The ones who ship 'em and see this as the moment where it all began aren't exactly an obscure crack-pairing group, so there might be a reason for the impression I got...
On an intresting Note, after I watched NGE with my sister (Not EoE, I'll wait until she's older for that...) and asked her which girl she thought should get together with Shinji, she gaped at me with large eyes and said: "Asuka and Shinji were in love? When? How so?" For the sake of Neutrality/accuracy, I pointed her towards the most obvious scenes that could be cited as proof and tried my best to explain the relationship dynamics to her. I have no idea how in the milky way she could overlook the obvious romantic setup there (Then again, my sister is relatively new to anime, she might've been unfamiliar with the concept of a Tsundere), but this reminded me that what is considered "obvious signs of attraction" is relative.
Sailor Star Dust: (Re: "...for all intents and purposes, holding hands.") Shinji and Rei first held hands/Shinji pulled Rei out of the Plug in Sadamoto's manga post-Operation Yashima. Evangelion Prelude decided to use that as a manga nod, I guess. (Prelude has a few Sadamoto manga nods: Shinji's rant to Misato about how she and Nerv are selfish is similar to something Manga!Shinji told Misato after Kaworu's death.)