The first filing is for "Bungie Aerospace", which Joystiq speculates could be linked to a re-branding of the studio following its split from Microsoft. Other speculation points to a piece of technology, which might be licensed out to other developers.
The second filing, made on March 8th is for "Marathon", the title of Bungie's second game and first hit. Halo fans will be the first to note that Halo and Marathon most likely occur in the same overall universe.
The upcoming Halo: Reach should be Bungie's last entry in the series, which is owned by Microsoft, before it transfers over to the Microsoft-owned 343 Industries. Bungie does, however, own the rights to Marathon. Could Bungie be gearing up to develop a new Marathon or is this just a re-filing to secure the trademark?
Update: To both filings, Bungie's community director Brian Jarrard told Shacknews, "No comment".