Markdown engines in C already exist, and have been ported to Plan 9 via APE. For proper integration this should likely be turned into a native parser, but that should be a relatively easy task.
Doing this for the Inferno wikifs would be a bit more work, as no Markdown implementation exists in Limbo today (although there are similar things). Markdown, especially the original definition, is a pretty simple definition, though, so this should still be well within the scope of a medium-sized GSoC project.
For a small- to medium-sized GSoC project,probably pick one or the other as a project submission (working on the other, at your own pace, would be a great way to stay involved after the summer!). Any extra time could be spent converting the existing pages (or, even better, writing a conversion program for others to use).
It is not particularly important that the language understood by wikifs be markdown, per se, but it would be very nice if it was one of the widely understood similar alternatives (rather than a new creation). It is more important that the language understood by the Plan 9 and Inferno wikifs implementaitons be the same (or, at the very minimum, one a proper subset of the other).
If you're interested in this project but need something of a smaller size, doing just the native Markdown interpreter in a form which could be used for the rest of the project would probably be a good fit.
The original writeup on Markdown, including the initial perl implementation.
Discount, a Markdown implementation with Plan 9 support (via APE) in the mainline tree.
MD4C, a simple Markdown parser written in C. It's not currently ported to Plan 9, but it's simple enough that it should be a good target for a native port.
textmangle, a Limbo implementation of a markdown-like library (with moderately different syntax).
Pandoc and MultiMarkdown are two possible extensions worth considering. There are lots of others.
Textile and reStructuredText are alternatives to Markdown which might be suitable, although neither is in as widespread use.
Anthony Sorace has a wikifs which produces gemtext in addition to HTML.