Thanks for reminding me

Some good points, thank you!

To rephrase what some of you said, basically rooks are better with everything else being equal since they have the ability to win a pawn as LeeRoth said. If they have loose pawns to attack (like in the game Chernin-Marjanovic) they are usually an even bigger advantage. Queen is only better if she has an attack of some sort or if the rooks can't coordinate effectively. And as Gerry said, she is better off if she has other minor pieces.

In the pure two rooks vs queen circumstance, a lot depends on who has the initiative, where the pawns are and where the kings are.  Generally speaking, the two rooks are very strong when they can be used to hunt down weak enemy pawns, support their own passers, and create mating threats vs the enemy king (esp when the king is on the edge of the board).  Another advantage of the two rooks is that you can often trade them for a queen and pawn (e.g., Rxf2/f7 vs a castled king) in order to get to a pawn-up king and pawn ending.  The queen can be better when the enemy rooks are disconnected or forced into passivity by the need to either protect their own pawns or stop the enemy pawns (esp when supported by the enemy king).   
Off the top of my head some famous examples include Karpov-Polgar in the Modern Main Line of the Benoni (the line with 9..b5 10.Bb5 famously ends up in two rooks vs queen ending), and Chernin-Marjanovic, Subotica Izt 1987 (a game analyzed by Dvoretsky in his writings).  There's also the famous line in the Dragon (Yugoslav w. 9..d5 10.exd5 Nxd5 11.Nxc6 bxc6 12. Nxd5 cxd5 13. Qd5 Qc7 14.Qxa8 Bf5 15.Qxf8).

I'm just wondering if there are any general rules of thumb when it comes to this situation. What happens if there are minor pieces, pawns on the board aswell? Anyone know on top of their head of any famous games that feature this imbalance?