Excitatory and inhibitory synaptic transmission use different neurotransmitters and receptors
Whether the result of synaptic transmission will be excitatory or inhibitory depends on the type of neurotransmitter used and the ion channel receptors they interact with. Different neurotransmitters can be very similar in structure but can have profoundly different functions.
Excitatory synaptic transmission uses a neurotransmitter called L-glutamate. This is a common amino acid used throughout the body to build proteins (it is also used as a flavour enhancer - mono-sodium glutamate!!!). However, in the CNS it is the major excitatory neurotransmitter. It interacts with glutamate receptors in the post-synaptic neuron. These receptors are ion channels that are permeable to sodium ions and thus generate depolarisation waves. Inhibitory synaptic transmission uses a neurotransmitter called GABA. This interacts with GABA receptors, ion channels that are permeable to negatively charged chloride ions. Thus opening of these channels makes it harder for a neuron to generate an action potential.In general (though not necessarily exclusively), neurons use only one neurotransmitter to 'send' information and are thus either excitatory or inhibitory - they are termed glutamatergic or GABAergic, respectively.
In addition to L-glutamate and GABA, there are a whole range of other neurotransmitters and their receptors (acetylcholine, dopamine, serotonin and many others) that also perform vital functions in the central nervous system, some of which are excitatory and some of which are inhibitory. The functional loss of these neurotransmitters and responsive neurons are implicated some of the most devastating neurodegenerative disorders such as Alzheimer's and Parkinson's diseases while Prozac, probably the best known anti-depressant currently in use, affects serotonin-mediated neurotransmission.