First, define what you want to do. And how much money you want to spend.
The results are most useful in supplementing or confirming data you already have or augmenting already existing conclusions. The test will NOT provide you with a family tree. If you don't already have a well documented family tree with at least some branches back 6+ generations, genealogy DNA testing will be of limited value.
Y-DNA - can only be taken by a male and only shows the father line. Your father, his father, his father and so on. No wives at all. That means out of 8 great grandparents, you get information on only one. A woman must have a father, brother or paternal uncle or cousin tested. This can prove a shared Most Recent Common Ancestor and prove a poorly documented or suspected father line.
If you already have a well documented family tree with both maternal and paternal grandfather lines known, I would get the 12 marker Y-DNA test from FamilyTreeDNA ($50) and upgrade to 37 or 67 markers if you find you need the information. Otherwise the information is stored for possible future use. If you don't know very much, join a surname DNA project at FTDNA and get a discount on the tests.
MT-DNA can be taken by either men or women, but only shows the mother line. Your mother, her mother, her mother and so on. Plus the mutation is so gradual that it only shows very deep ancestry, thousands of years ago. It is rarely useful for genealogy. The full sequence MT-DNA test from FamilyTreeDNA (costing about $300) has a 50% chance of matching closely enough to trace the mother line but ONLY if a close cousin has also taken the same test. And you ONLY have information about one line out of all those great grandparents. It think it is a waste of money in most cases.
Autosomal or AT-DNA can be taken by either sex and potentially covers distant cousin matches up to 6-8 generations. Right now Ancestry DNA has the largest base of family trees matched with DNA results - a real plus. They do not offer chromosome matching and similar data tools so the results cannot be used as any kind of proof - that is a real negative. FTDNA has fewer family trees and their test is much more expensive but they do offer a wealth of matching tools. And as of May 1, Ancestry DNA results can be transferred to FTDNA (probably for $89).
I guess I would go with Ancestry's $99 autosomal test, and transfer the results to FTDNA so you would have a much larger pool of possible matches and useful tools. Then hope that Ancestry provides the tools necessary for serious genetic genealogy sometime soon.