Recall that usual estimates of individual effect variance are calculated under assumption that the regression disturbances are not serially correlated. Hence if you get negative estimates, you should check whether serial correlation is present.
If serial correlation is not present then you should test whether individual effect is present at all. If you cannot reject hypothesis that it is zero, this means, that there is no individual unobserved effect and you can use simple pooled regression.
If the serial correlation is present this means that the usual random effects estimator is not suitable. You should then either include additional variables into your model, or use a GLS approach. The standard fixed effects estimator would be consistent in such case, but you should then use robust standard errors, since serial correlation would still be present.