Example 1: Instead of having the students memorize phylogenies, and basically just accept them as a given, have the students in a lab actually reconstruct a phylogeny for a group of organisms (this could be done with major animal phyla, or with major groups of embryophytes). In the first lab, the students put to use their knowledge of morphological terms and structures, and record observations on organisms available in lab (with some information provided to them, to make the exercise feasible), and in a follow-up lab they delimit characters and states, construct a matrix, and practice forming groups (based on parsimony, grouping by synapomorphy). Then, they compare their phylogenetic hypotheses with accepted phylogenetic trees (based on DNA sequences and additional characters) and discuss where their phylogenies are similar and where they differ.
Example 2: It is also useful to organize the information on plant and animal structures/functions (e.g., the circulatory system, respiratory system of animals, internal conduction of water in plants, etc.) by placing it within a phylogenetic context. Thus evolution, and evolutionary pattern, are fully integrated into the information about how animals or plants "work." This approach allows the teacher to integrate structure/function questions with evolutionary pattern and process.
Example 3: Role play parts of the cell (not evolutionary biology, but a good way to learn the cell): This can be an outdoor track event where DNA (one person) has a code sheet that needs to be translated. mRNA (another person) converts and carries a message to the ribosome who decodes it. Organelles are stationary. Vacuoles transport products. The point is to decode and produce proteins (built out of legos, bagged (golgi body), with sugar (mitochondria)). A group of cheerleaders (chloroplasts) is responsible for running around the cell and encouraging their team. In the end, they all get mitochondria awards (sugar).