Warner Brothers are to release two Matrix Trilogy box sets on HD DVD on 22nd May. One set will contain the three films, whilst the Ultimate Matrix Collection will feature over 35 hours of bonus material on five double-sided discs.
As you'd expect from Universal Warner Bros, a Blu-ray release will happen - but not for a while. Due to the amount of interactive features found on these releases, many Blu-ray players can't yet handle it.
Unlike HD DVD's IME (In Movie Experience) that allows for picture-in-picture (PiP) features, The BD-J functionality required to give Blu-ray players a similar feature set isn't yet universally available, though the Blu-ray Disc Association is planning to change that.

Universal? There wouldn't be a BD version if it was from Universal.
Warner ;)
Slip of the tongue, sorry. I said it right the first time.