Both Januvia and Byetta work on the Incretin pathway, Byetta acts like GLP-1 and Januvia extends the life of your natural GLP-1. Byetta needs to be injected twice daily and needs to be kept cold, although a once a week injectable will be available soon. Januvia is an oral medication. Byetta causes dramatic weight loss in about 1/3 of patients taking the larger dose. There is little or no weight loss with Januvia. Byetta seems to lower HbA1c more than Januvia but the results in any one individual may be different.

Not aware of any head-to-head trials of Januvia vs. Byetta, but I think the results would be pretty obvious. Januvia essentially prevents the breakdown of GLP1 whereas Byetta is essentially GLP1 given at higher than the levels that are produced in the body. It would be like giving someone a drug that prevents insulin breakdown vs. giving someone lots of insulin in the form of an injection---the latter will tend to win that race.
Along the same lines, you would expect more side effects with the Byetta than Januvia and we do---a lot higher risk of side effects including nausea.
THat has been very important in my practice and brings up an important part of evaluating drug effectivness. A drug can be shown to be clinically effective in meeting one target (lowering A1c) but essentially useless if a large portion of the population can't tolerate it (rob Paul to pay Peter).
Januvia is much easier to use but less potent. Because of it's relatively week potency and high costs I have reserved it for invididuals with very mild A1c elevation and who can not tolerate metformin and/or sulfonylureas (glipizide).
Byetta I also tend to use sparingly because of it's high costs and the fact that the other injectable medication (insulin) works even better. Weight gain (more than weight loss) tends to drive my consideration for Byetta and also patient preference after all of the above is explained.