The performance hit when running an odd number of tasks isn't just limited to the X2 and is common to the 840D and the 540J. What is interesting is that the 840D and even the 540J can match the X2 4800+ in fps when running 3 other heavy tasks. It's not like the X2 "only takes a hit" for the 3rd and 5th program as it is still 40 fps down from its peak and is still slower than the 840EE under four tasks. Whether the 840EE loses some to every additional program or not, the drop off in performance for the X2 4800+ after 2 tasks is still steeper. The 955EE would improve upon the performance of the 840EE as while it may not correct scheduling conflicts, the doubled cache and expanded FSB will relax the resource crunch of HT.
Even if you play around with the affinities, it's likely that the 840EE or the 955EE will still be ahead in overall performance. Allowing the game to run on a dedicated core will allow the X2 4800+ to pull ahead in fps as we know that its superior in dedicated game performance. However, the performance of the background applications running on the single remaining core will suffer. The performance of the A64 4000+ falls considerably when a second task is added, while the 540J manages to perform admirably due to HT. Discounting running 3 or 5 applications since its deemed unfair, the 540J likewise performs better than the A64 4000+ when its running 4 heavy programs which is what that 2nd core of the X2 4800+ would be doing once the 1st core is dedicated to the game.
Games may be controversial since, as you say, if you really want gaming performance you can dedicate a core. However, looking back at the Anandtech comparison, the 955EE still appears superior in terms of heavy multitasking. Running 4 programs, avoiding the X2s weakness with odd numbered tasks, the 955EE manages to complete a virus scan, a MP3 encode, a Windows Media encode, and an unzipping more than 15 seconds or nearly 10% faster than the X2 4800+.
In addition, in both reviews the Intel processors were at a slight disadvantage. While the X2 4800+ was given enthousiast DDR 400 with low latencies of 2-2-2-5 for Digit-Life and 2-2-2-7 for Anandtech, the 840EE received DDR2 533 at 3-3-3-8 and the 955EE received DDR2 667 5-5-5-15. Better performance could have been achieved with DDR2 667 at 3-2-2-8 or synchronous DDR2 800 at 4-3-3-12 for the 840EE and DDR2 889 at 4-4-4-12 for the 955EE.