At the Zeitgeist hackfest we designed a bar which pops down at the top of the screen and shows recent documents.  Assuming that I understand the concept of activities, that bat could serve (with a few modifications) as a replacement for the window list. Here's how it would work:
1. Instead of showing all recent documents, the bar would show recent documents which are related to the currently open documents. For example, if I have a pdf file open then the bar would show all of the other reference papers whether they're still open or not.
2. Each activity could show it's own bar.
3. The bar could be hidden by default or it could have a minimized view - something like the windowlist - that would show the documents. (Again, even if they're not open.)
4. When I use the term "Documents" that doesn't need to refer only to documents. When applicable, an application or even a window could be considered a document.
For example, most games don't open any documents so we can just show the game as a document-like item. (Which can form part of an activity.)
It might also make sense to show each Firefox window as one document so that the list of documents doesn't get overfilled with each tab that the user has open in Firefox. (If people learn to group related tabs into one Firefox window then that could work very well.)
5. In Zeitgeist, a document doesn't need to refer to a file on your computer. For example, it can also refer to tomboy notes and websites. In the future, we're going to even include Google Documents, Flickr pictures, and Delicious Bookmarks in our document database. All of these can appear in the same documents bar taking activities (collections of related documents, if I understand correctly) to a whole new level of usability.
A few caveats:
1. Zeitgeist's support for determining which documents are relevant to one another is still experimental and hasn't yet had a stable release.
2. We figure out which documents relate to one another (in the shell's terminology: which documents form an activity) based on their usage. (E.g. was one document opened while another document was open? Did the user switch often between one document and the other?) This means that there's no way of immediately telling what activity a new document belongs to when it's opened for the first time. To solve this, we can show the document in all of activity bars until we can determine which one it belongs in.