Search -- Getting to the point we need this already, IMO
pagination on forum displays -- Same as above

Show New Forums Only / Collapse forum categories -- I assume you'll be adding more for[a/ums/ibuses] soon. One of these will (IMO) have to be done as soon as the total list of for[a/ums/ibuses] is longer than one screen. If both work, even better, but either should be sufficient.

Administrative interface -- If this is what we need to get more admins, I think you're about to need this pretty badly. (Unless you plan on making this your full-time gig.)

Mail-on-response -- I can only see using this when I post a very specific question in Area 51, but for that it would be great.

Mark forum category read -- For the people who would do this (eg: skipping the Open category) I think this would work better as a user-configurable option. From the user settings, select not to see that category. Since (I suspect) the list of active for[a/ums/ibuses] will be somewhat dynamic, I don't think that evel of control from the user settings would be useful.

Page titles -- Does add useful information, and shouldn't be too difficult.

Fix CSS usage -- As long as the page still works without CSS, this can wait. Although, I would prefer that all formatting that is done use CSS. No point in having to go back and take out all the font tags once people finally get standards-compliant browsers.

Alternative nesting spacing on showContent -- I don't have any problems with the current settings. But if there are setups where this is a problem, it's pretty important.

User-selectable caching controls for dynamic pages -- Same as above. I'm on a fat pipe and don't see any problems. I'll let you know if using it from home changes my mind.

Parent thread listing above content -- Nice, but it can wait
Don't show lrpd for Anon users -- Same as above
Stats -- Same as above

Duplicate post prevention -- Has this been a problem? I haven't seen it, but it should be fixed eventually.

NNTP Gateway -- Wouldn't change the way I use this, but it would make the overall package much more versatile

Killfiles -- Until/unless we get about five times the traffic we do now, I can do this by just not reading all of it. I don't see the need yet.

The rest seem like code maintainability more than usability.
Single SQL for forum list
Factor posting functionality (quote buttons disappearing, etc)
Move authentication to Login Manager