Wow...you guys hit the top ones
fast. My first thought was Starnet blocking. 2nd thought was the archaic late-90's-era websites that all airlines seem to use.
The inability to easily query availability across an alliance and book any award online is a major pain. If the agent has access to the data, why don't I? Heck, all of ANA's travelers can view the information! (Not sure if they can book or not.)
In the hotel world, the inability to query an offer, award, or promotion across an entire metro area is annoying. Why can't I easily look and see exactly which Starwoods have an SPG50 rate for this weekend in Manhattan? Marriott is a bit better in this regard...although they don't have a direct analogy to the SPG50.
In the rental car world, the entire industry is my pet peeve.

It seems that it's falling apart at the seams. The major agencies initiated their frequent-renter programs some years ago but none have been truly forced to innovate or provide passable customer service beyond that. Perhaps it's because most of their profits come from large corporate contracts...I don't know. But even previously-good systems like #1 Club Gold and Emerald Aisle seem to be breaking down. It's not just the old cars - which I can kind of understand in 2008-2009's credit market - but the
basic functions of the operations are failing everywhere.