The following papers from Selim Akl may be of interest and relevant to the discussion:
Akl, S.G., "Three counterexamples to dispel the myth of the universal computer", Parallel Processing Letters, Vol. 16, No. 3, September 2006, pp. 381 - 403.
Akl, S.G., "Even accelerating machines are not universal", International Journal of Unconventional Computing, Vol. 3, No. 2, 2007, pp. 105 - 121.
Nagy, M. and Akl, S.G., "Parallelism in quantum information processing defeats the Universal Computer", Parallel Processing Letters, Special Issue on Unconventional Computational Problems, Vol. 17, No. 3, September 2007, pp. 233 - 262.
Here is the abstract of the first one:
It is shown that the concept of a Universal Computer cannot be realized. Specifically, instances of a computable function F are exhibited that cannot be computed on any machine U that is capable of only a finite and fixed number of operations per step. This remains true even if the machine U is endowed with an infinite memory and the ability to communicate with the outside world while it is attempting to compute F. It also remains true if, in addition, U is given an indefinite amount of time to compute F. This result applies not only to idealized models of computation, such as the Turing Machine and the like, but also to all known general-purpose computers, including existing conventional computers (both sequential and parallel), as well as contemplated unconventional ones such as biological and quantum computers. Even accelerating machines (that is, machines that increase their speed at every step) cannot be universal.