Please read Catherin Buetefisch's recent work, as well as Joseph Classen's. This will give you a good working background of the effects of TMS on motor rehabilitation. Marnie Naeser's work with aphasic stroke survivors has indicated that targeted repetitive TMS may modulate contralesional recruitment and improve therapy outcome.
As all of us know regeneration of cns depends on many variables and new techniques such as rTMS are just in a begining way to make significant changes in cns. but in some cases I personally have seen good results. Note that still its not a miracle. rTMS can stimulate inhibitory or excitatory changes in the special area you use it on cns. the maintenance and functional output of these changes has to be more investigated
Transcranial magnetic stimulation (TMS) basically stimulates or inhibits the underlying cortical area. Stimulation or inhibition though depend on the frequency of stimulation used high( above 5 Hz) or low (below 5 Hz). Stimulation areas depend on the CNS condition a patient is suffering from or site or stage of pathology. For e.g in case of parkinson's patient if the patient has more of motor symptoms motor cortical areas may be choosen and if more of depression then frontal cortex may be the area of choice.
This is an FDA approved procedure for treatment of depression but phase III trails are underway for stroke and parkinson's etc.
Molecular studies so far on mice and non-human primates are indicative of changes in the cortical plasticity (short term as well as long term). These results are also seconded by fMRI and PET studies in humans as well as primates.
Concerning stroke rehab, there is a whole field in development for combining rTMS with movement therapy. RTMS is used for priming the brain to influence motor learning (see Schabrun & Chipchase, 2011), based on the concept of rapid brain metaplasticity (see Gentner et al., 2008). I hope this will help!