Well, actually, that's not technically true. SCOTUS struck down section 3 of DOMA, which prevents the federal government from giving marriage benefits to same-sex couples. Section 2 of DOMA, which permits a state without same-sex marriage to deny recognition of same-sex marriages from other states, is still in force, at least for the moment. But section 2 is a legal nightmare.
Ordinarily, when you sign a contract, its validity is a federal matter. Either it is valid in every state, or it is valid in no state. Marriage no longer works that way. Suppose two men are married in New York. Under Windsor, the federal government now recognizes that marriage, and extends tax and other benefits to them. But then they travel to Texas, which does not recognize same-sex marriage. Suddenly, they are single. Or are they? It's unclear whether the federal government should apply New York or Texas law in determining benefits. But clearly, as far as the state of Texas is concerned, the men are single.
Next, they go to California, where (it would seem, given the outcome of Perry) same-sex marriage is recognized. Are they married again? Did their original marriage contract from New York survive this transition? Or did it vanish at the Texas border? If it did, then that suggests a contract has been dissolved without any legal process, which seems troubling to me. If it didn't, then why wasn't it in force in Texas? Was it in abeyance somehow?
If the contract was in some kind of legal limbo, but not actually dead, this suggests a rather interesting situation. A contract is valid but unenforceable thanks to a provision of Texas's state laws. State laws aren't allowed to impair contracts under the Contract Clause. But maybe Congress can authorize them to do so via DOMA. Let's consider that.
Section 2 of DOMA is as follows:
No State, territory, or possession of the United States, or Indian tribe, shall be required to give effect to any public act, record, or judicial proceeding of any other State, territory, possession, or tribe respecting a relationship between persons of the same sex that is treated as a marriage under the laws of such other State, territory, possession, or tribe, or a right or claim arising from such relationship.
I find the term "required" rather interesting in this context. Required by whom, exactly? If it means "required by the courts," then this seems an entirely inappropriate attempt to dictate the outcomes of court cases. Under the doctrine of separation of powers, Congress isn't supposed to be doing that.
On the other hand, if it refers to constitutional requirement (i.e. "required by the constitution"), that really isn't much better. If the constitution says one thing, and the law says something else, generally the constitution wins. Laws aren't allowed to dictate how the constitution is interpreted; again, that's a matter for the judiciary.
Just about the only "required" that I believe Congress could refer to here would be "required by federal law." But if that's what the statute means, I don't think it will have any effect whatsoever. I'm not aware of any attempts by federal law to require Texas to recognize a same-sex marriage.
In conclusion, it's not at all clear to me that DOMA section 2 even needs to be challenged on due process and equal protection grounds. It could fall to separation of powers.
Updated: It's been brought to my attention that the contract clause is inapplicable to marriage contracts under longstanding precedent. This is why I'm not a lawyer. All the same, there are quite a few interesting questions raised above, so I'm leaving this post up.