Crash (a film set in LA were most of the Academy members live and/or work) beating Brokeback Mountain (or Good Night and Good Luck which I also thought was better - not Munich though, how they made a film about such an emotive topic so dull I'll never comprehend) and Helen Hunt (an American up against 4 brits) beating Judi Dench both really annoy me. Also Chicago beating the Pianist was bizarre.
I was disappointed that Pan's Labyrinth lost out last year but The Lives of Others is just as worthy.
Also, I am still completely bemused by the win of Driving Miss Daisy as best film (it's a nice enough film and Jessica Tandy was excellent but come on!) and Halle Berry's win as best actress, I watched Monster's Ball on the strength of that win and regretted it.
There are so many issues with the way Oscars are awarded which lead to these problems. Given that the largest number of people voting are American, they are generally favoured hence Helen Hunt and Marisa Tomei's victories. I was actually surpised Helen Mirren won last year although there was a certain amount of inevitability to it.
Since actors make up the bulk of voters, actors in non-acting roles (like Kevin Costner, Robert Redford, Clint Eastwood and Mel Gibson who all won Oscars for directing but not acting) do well.
Sometimes they are awarded to correct past mistakes (Judi Dench's win, Martin Scorsese's win for the Departed which I'm not sure was necessarily the best film last year but his oscar was long overdue) or to reward a body of work rather than that performance (thinking specifically of John Wayne here).
The films made by the bigger studios tend to have the money to campaign for the votes of Academy Members, sending their films to old people's homes and sending out reps all over the place to convince or even bully people to vote for their films. It has been suggested that this is part of the reason Miramax has done so well.
Given that all of the awarRAB are voted for by every member of the academy very often they just tick a film that they like in several categories whether they are the best in that category or not. This affects mostly the technical awarRAB and is not repeated at the Baftas as most of these are chosen by a panel of professionals not the whole academy.
They also like to appear cleverer and deeper than they are (possibly why Shaespeare in Love did better than it had any right to) and there are definitely themes that they like to reward (illness either mental or physical being one of them - both of Tom Hanks oscars covered here, surely a much overrated actor - he only ever portrays Tom Hanks).
Finally they are affected by events and opinions in the outside world. The Academy often plays safe rather than risking public scorn (hence Crash's win). Also, Eddie Murphy who was practically a shoe in to win Best Supporting Actor last year lost out largely because of the disgusting Norbitt.