-Pay extra towards the student loan How fast could you pay it off? If a few months, this would be my choice. You're getting a great risk-free rate and can then free up the cash flow for your other goals. If it would take years, it would mean putting your other goals on hold.
-Increase our emergency fund This depends on your risk - are your jobs stable? Do you have good health insurance? Do your parents have enough assets and insurance to take care of themselves?
-Put money away for a down payment for a house (we hope to buy in 2-3 years) This is a good choice. The more cash you have, the more options you have to avoid PMI, buy a fixer-upper, etc. Again, this depends on how much extra income you have each month and how much the house you'd want to buy would cost, etc.
-Put money in a Roth IRA (my wife's 401k has really high fees and we will definitely be in a higher tax bracket when we retire, so the Roth seems to be the way to go for extra retirement money after we take advantage of the full 401k match) IMO you should both be saving for retirement. Roth IRAs are a good choice because you can take your contributions back out at any time without tax or penalty. If nothing else, consider opening Roth IRAs for each of you at a bank and putting your emergency fund money in there. ING (now Capital One 360) offers IRAs and your money is held inside an insured savings account. It's there if you need it, but you are taking advantage of the tax-sheltered retirement space if you don't.