I normally won't bother with a 5 month old community wiki, but someone else bumped it and I couldn't help but notice that the significant majority of the examples are highly algebraic. I wouldn't want the casual reader to go away with the impression that everything is defined correctly all the time in analysis and geometry, so here we go...
1) "A smooth structure on a manifold is an equivalence class of atlases..." Aside from the fact that one hardly ever works directly with an explicit example of an atlas (apart from important counter-examples like stereographic projections on spheres and homogeneous coordinates on projective space), this point of view seems to obscure two important features of a smooth structure. First, the real point of a smooth structure is to produce a notion of smooth functions, and the definition should reflect that focus. With the atlas definition, one has to prove that a function which is smooth in one atlas is also smooth in any equivalent atlas (not exactly difficult, but still an irritating and largely irrelevant chore). Second, it should be clear from the definition that smoothness is really a local condition (the fact that there are global obstructions to every point being "smooth" point is of course interesting, but also not the point). The solution to both problems is to invoke some version of the locally ringed space formalism from the get-go. Yes, it takes some work on the part of the instructor and the students, but I and a number of my peers are living proof that geometry can be taught that way to second year undergraduates. If you still don't believe there are any benefits, try the following exercise. Sit down and write out a complete proof that the quotient of a manifold by a free and properly discontinuous group action has a canonical smooth structure using (a) the maximal atlas definition and (b) the locally ringed space definition.
2) "A tangent vector on a manifold is a point derivation..." While there are absolutely a lot of advantages to having this point of view around (not the least of which is that it is a better definition in algebraic geometry), I believe that this is misleading as a definition. Indeed, the key property that a good definition should have in my opinion is an emphasis on the close relationship between tangent vectors and smooth curves. Note that such a definition is bound to involve equivalence classes of smooth curves having the same derivative at a given point, and the notion of the derivative of a smooth curve is defined by composing with a smooth function. So for those who really like point derivations, they aren't far behind. There just needs to be some mention of curves, which in many ways are really what give differential geometry its unique flavor.
3) The notion of amenability in geometric group theory particularly lends itself to misleading definitions. I think there are two reasons. The first is that modulo some mild exaggeration basically every property shared by all amenable groups is equivalent to the definition. The second is that amenability comes up in so many different contexts that it is probably impossible to say there is one and only one "right" definition. Every definition is useful for some purposes and not useful for others. For example the definition involving left invariant means is probably most useful to geometric group theorists while the definition involving the topological properties of the regular representation in the dual group is probably more relevant to representation theorists. All that being said, I think I can confidently say that there are "wrong" definitions. For example, I spent about a year of my life thinking that the right definition of amenability for a group is that its reduced group C* algebra and its full group C* algebra are the same.
4) Some functional analysis books have really bad definitions of weak topologies, involving specifying certain bases of open sets. This point of view can be useful for proving certain lemmas and working with some examples, but given the plethora of weak topologies in analysis these books should really give an abstract definition of weak topologies relative to any given family of functions and from then on specify the topology by specifying the relevant family of functions.
I'm sure I could go on and on, but these four have proven to be particularly difficult and frustrating for me.