"Rational Basis" is the test that the Massachusetts Supreme judicial Court [as compared to its Supreme Executive Court?] argued that the ban on same sex marriages did not meet. See, for instance, the discussion in this debate on the subject currently found in the New Republic. The reply is that it is "reasonable" (if not necessarily correct) or "rational" to argue that special benefits to heterosexual couples (e.g., marriage) further the states' interest in advancing the best way to raise children (i.e., via a man and a woman, preferably by natural means). I think this makes a valid point, but obviously, it depends on what you mean by "rational basis." Clearly, if this was some law regulating widgets, the test would be less strict.
Let's be honest here. Justice Rehnquist sometimes asks when an advocate talks about how a law is "irrational," if s/he means the legislators who wrote it were basically crazy or something. The comment is not only used by conservatives; John Hart Ely (recently deceased) also often noted that it is rather hard to think of a truly irrational law. The only reason a law is not "rational" is because certain interests are deemed illegitimate or the burden inflicted is deemed to harm a protected class or fundamental right. And, this is exactly what is at stake here: classification by sexual orientation and sex/gender is treated differently than classification by say intelligence, and marriage is fundamental civil right. So, the obstacles the state has to climb over might not be "strict" (really hard, as if free speech was at stake), it is more than "rational basis." I'd call it (no, I didn't originate the term) "rational basis plus."
The habit of pretending or assuming things are less complex than they really are is not just present in cases like this. For instance, many think the President's general practice is to act irrationally. This leads to people arguing that on subjects like invading Iraq that there is some method to his madness. And, the critics look silly. The better path is to show that your opponents' arguments are on balance unreasonable or problematic. For instance, if you think a "compelling" case is needed to go to war, maybe the case was mixed, but not compelling. You need not exaggerate either side (those totally assured of their validity are leading themselves to the path of ruin or the misguided assurance they denounce in their foes) to win in the end. In fact, you very well might do a better job not doing so.
And, so would be the case in the same sex marriage case ... yes, in some way perhaps the discrimination is rational or enough so that the courts should not second guess the legislature. All the same, given the interests at stake, this is not enough. A closer, but not even a very close, look will show the state's case is a bit too weak to pass muster. Or maybe not ... but this is what is really being done here, and it is misguided to pretend otherwise.