Although I have to declare some self interest in this, synthetic CPU benchmarks are useful becuase,
A) They can generally be automated and in most cases can run fairly quickly. So the additional overhead for Tom's of including the synthetics in an automated suite is low.
B) They pretty much all have a free trial, or are totally free.
C) They are (for the most part) small downloads with a easy install and run a standardised test.
D) Users reading Tom's site can compare their home / work systems with Tom's results. If you are testing with Office suites, 3D suites and even games it can be difficult to reproduce the test results as you won't have the same set of test files & scripts (unless Tom makes all this available).
E)Patches to games and other applications can effect performance. WoW now using all cores being a good example. So getting and keeping the exact version of an app becomes critical for a fair comparision. In many cases old releases of commerical applications are not available to the public. Meaning results can not be reproduced by the public once some time as passed. The synthetics are more careful that small patches don't effect performance and generally make old releases available.
E) Some of the above suggestions would not make good CPU benchmarks by virtue of the fact that they are not CPU bound. Microsoft Security Essentials, Office applications and even Visual Studio can often be disk bound rather than CPU bound. Some of the other suggestions like Photoshop, Flash, SETI, etc might also be impacted by the 2D video performance of the video card or networking performance. The synthetic CPU benchmarks don't generally have much if any depenance on the video card & disk.
F) The synthetics can in general use all cores (or a configurable number of cores). By the end of 2011 it will be common place for CPUs to have 8 to 16 cores (with HT). So it is important to have at least some of the benchmarks pushing all core to their limit. What current games are going to use 100% of 16 cores?
G) The synthetics are actually not all that synthetic in many cases (ignoring the simple integer and floating point tests). They often use real world algorithms pulled from real world applications.
So I would be in favour of have some synthetics in the list.
PCMark, SiSoftware, PerformanceTest CPUMark, SuperPi, etc..