I've got 14 cards on linux and 4 cards on windows. I'll run it down for you from what I noticed.
--------- Positive--------------
1) Linux has superior power management.
a1) Running 6970, 6970, 6950 in windows draws 1100 watts in windows.
a1) Running 6970, 6970, 6970, 6870, in linux draws 1100 watts.
2) Linux has drastically less CPU usage. I need at least a 3x core at 3 GHz to run 4x 5850s in windows. On linux i disable all cores but 1. I now run a 2.7 single core with 4x 5850s.
3) Remote management is vastly easier in linux. Multiple SSH etc.
4) Hash per second is virtually the same.
5) Incredibly stable. I think I've had a 4 machines up for 2-3 weeks now.
6) Can run ATI Stream 2.1 & 2.4 at the same time. Allowing 6xxx and 5xxx on same system.
----- THE DOWNSIDE ------------
Voltage tweaking and overclocking are terrible.
1) 6950, 6970, 6990 cannot be overclocked in linux using AMDCtrl. Any overclocking cause the mhash to lower.
2) Non-reference 5xxxx are very difficult to overvolt. Easy to overclock under stock voltage. Lowering memory is difficult.
3) Basically if you cannot flash your bios then you will NOT be able to overvolt your card in linux. (You can still overclock at stock voltage.)
4) Fairly difficult to get wifi cards working if you don't get the right one.