The SSRI's are some of the most commonly prescribed and taken medications in all of medicine-- while there is a large contingent of 'psychiatry haters' and 'antidepressant haters' out there who blame them for all of their ills, I am not aware of any evidence for long-term side effects. I do not mean to classify you into the categories of people I mentioned, by any means.
There are discontinuation symptoms with some of the SSRIs and SNRIs, depending on the half-life of the medications. Paroxetine and Effexor have the worst 'discontinuation-emergent symptoms', and Prozac (fluoxetine) probably has the least.
The 'brain zaps' and flu sensations are most common after discontinuation; the way they are usually handled is to put the person on fluoxetine (4 bucks at WalMart or Target) for a month, then stop the fluoxetine-- it tapers itself over weeks or months.
As for the long-term effects, I just have never seen evidence for permanent effects on neurons-- the medications bind to the re-uptake site in a reversible manner, and do not do anything permanent. Just as much of the antidepressant effect is due to placebo, many of the side effects are as well-- that doesn't make them any easier to tolerate, but does suggest that the proper way to treat them is for your therapist to work with you to try to redirect your thoughts as much as possible.
Jeffrey T Junig MD PhD
Owner, Fond du Lac Psychiatry
Asst Clinical Professor of Psychiatry
Medical College of Wisconsin