There are several studies of what premedication should be used for intubation of the newborn. An analgesic or anesthetic agent should be given in to reduce pain, which also reduces the adverse physiologic consequences of the intubation.
Several studies of different agents exist, and one of the most used agents in clinical practice is morphine. A new study (Norman E, Wikstrom S, Rosen I, Fellman V, Hellstrom-Westas L: Premedication for intubation with morphine causes prolonged depression of electrocortical background activity in preterm infants. Pediatr Res 2012.) examined a subset of a small RCT who had prolonged EEG monitoring. The RCT compared thiopental plus remifentanil to morphine. The thiopental/remifentanil group had EEG suppression after the meds which lasted less than 3 hours; after morphine the suppression lasted more than 24 hours. Also blood pressures were lower in the babies who received morphine.
Morphine is the one agent that has not been shown to improve physiologic responses to intubation, probably because of an onset of activity at 10 to 15 minutes, and usually the intubation has been performed prior to this interval. Fentanyl reduces those responses, as does remifentanil. An RCT comparing remifentanil to fentanyl plus succinylcholine, showed the same effect on physiologic responses of the two regimes.
I don’t know if the thiopental in the regime of Normal et al is really necessary, remifentanil alone is an excellent analgesic, and reduces the physiologic responses with a very short duration of action (as far as we know, in the very preterm there is a need for more data) . Some babies are expected to be extubated very quickly after surfactant and there are concerns regarding the duration of action of fentanyl, now I have never found this to be a problem, as fentanyl causes little respiratory depression, but I do think that remifentanil, with its very short duration of action of a few minutes would be preferable if we had more data. Is it necessary to add a hypnotic agent? That might turn out to be a philosophical question; I think it will be hard to prove an advantage of adding a hypnotic agent to an effective analgesic. (A nice recent review of remifentanil in the newborn: Penido MG, Garra R, Sammartino M, Pereira e Silva Y: Remifentanil in neonatal intensive care and anaesthesia practice. Acta Paediatr 2010, 99(10):1454-1463.)
Neonatal Research 
Unfortunarely, besides the scarcity of data, remifentanyl is significantly more expensive than fentanyl. Every time I asked for it, even more in the current cost containment era, the answer is absolutely not.
It is true that remifentanil is about 40 times more expensive than fentanyl, but fentanyl costs about 50 cents for the amount you need to intubate a newborn, depending on where you are, 20$ might be a big deal for the intubation, but the anesthetists often use hundreds of dollars worth!
How about Propofol?
I really think that the common practice of using opiates for anesthesia in neonatology( be it intubation or large surgeries) is strange….Are we ok with it?
I think Propofol may be a good choice, we just have very little data, especially for the tiny babies: Ghanta S, et al published a study in Pediatrics in 2007 (Propofol Compared With the Morphine, Atropine, and Suxamethonium Regimen as Induction Agents for Neonatal Endotracheal Intubation: A Randomized, Controlled Trial) which showed that propofol seemed better, but then again morphine isn’t a good choice to compare against, and the only study I know about used propofol and remifentanil, which showed no difference to midazolam and remifentanil. So I think we need more information before starting to use propofol.