Posted this previously on Cubits, but here it is again:
I use Microsoft Excel (any similar program would work) to create a map of my iris beds. Each year, I create two new "sheets" for each bed, one in the spring to just to track which varieties bloomed or didn't and another in the fall to track how they are doing. For example, the attached map (not the best quality image, but hopefully good enough) is one of the beds from fall 2010. The yellow shaded blocks indicate irises that I am concerned about how well they are growing, orange blocks are irises that are growing fine but have so far failed to bloom, red blocks indicate irises that aren't growing well and have never bloomed, green stripes indicate irises that were divided this summer.
This way I can easily keep track of where different varieties are, where they used to be, when they were divided, which years they bloomed, which years they didn't, a general idea of how well they grow, etc. The coding possibilities are almost endless.
I don't use markers as I don't like the way they look in the garden.
I also keep track of which varieties I've acquired, how much I paid, when, from which grower, etc. in a separate Excel file. It also serves as a wish list for the future.