Can we look at R&D cards that are trashed by virus install?
I'll start by saying that Fantasy Flight Games has never officially commented on this, but there are a few threads on both their forums and Board Game Geek that come to the same conclusion.

The top card of the R&amp;D gets trashed face down. This thread on Board Game Geek comes to this conclusion based on a few sections of the rules:


Page 6 talks about cards going into the Archives face up or face down. Notice this also addresses whether the Corp can look at face-down cards in their Archives. 


  Some cards enter Archives faceup, and some cards enter
  Archives facedown. Facedown cards in Archives should be
  oriented horizontally so that the Runner can easily see them.
  Both the Corporation and Runner may look through the
  faceup cards stored in Archives at any time, and do not need to
  maintain the order of its cards while doing so. The Corporation
  can also look at the facedown cards in Archives at any time; the
  Runner cannot.

On page 13:


  When installing a card in a server, the Corporation can first
  trash any cards already installed in that server. Trashed cards go
  to Archives faceup if they are rezzed, and facedown if they are
  unrezzed.



User Mat Nowak concludes


  [A]s you can see from all this, cards trashed by Noise's ability enter the Archives face down in a horizontally oriented pile. (This is because the card in question enters the Archives from an unrezzed state).


Other users in that BGG thread tend to agree with him. This is also discussed at the Fantasy Flight Games forum here, and users tend to agree that although there's no actual rule for this, it is the logical way to handle the Noise virus.

The way it looks like it should be handled in all situations based on the page 13 rule: If the runner knows what the card is when it goes to the Archives, it goes in face up; otherwise it is face down. Also remember that cards that are face down in the Archives are turned horizontal so the Runners knows if there are cards they haven't seen in there.