Okay, so.
In the forum, if you reply to comments, it currently threads out in a tree view sorta thing. Do we want that, or do we want a more standard thing where everything's all in one list, where you use quote tags to reply to stuff specifically? (which I personally prefer.) You can do that by going to Administer -> Content -> Comments, then clicking Settings, and changing the setting under Default Display Mode. Then install the Quote module, which will allow you to quote things.
Unfortunately, I can't find any way to add a "new posts list" to the forum, which is really quite essential, (I pretty much live in that list on all the forums I visit). If you can find a module to do it, or you can whip something up with your magical code skills, that would make me haaappy. 
Also, with the way the pathauto settings are now, the title of threads appear in the urls for those threads. I personally don't like that, as it means regular users have control over the urls of pages, which means long-winded thread titles cause google to associate keywords less effectively, and it also means you have nasty looking urls for threads posted by spambots.
Anyway, you can change that in the Pathauto settings, under Node Path Settings. I'd suggest using "/forum/[catpath-raw]/[nid]" for forum topic urls. If you don't mind having thread titles in urls, I'd make it "/forum/[catpath-raw]/[title-raw]". You should probably go through everything else in the Pathauto settings and make sure all the settings are what you want.
Um, yeah. That's all I can think of for now.
Heya,
Thanks for all the tips. I'll steadily work on them.
As for the new posts, I'll have to think about it. Possibly the Views module might be able to whip something up along those lines. I could otherwise reverse-engineer the Recent posts block.