I'm right there with you on WP48, nick (as you know). Any stat that says Andris Biedrins is a significantly better player than Paul Pierce is not a stat I pay much attention to.
As for "per minute" stats, I think they serve a purpose, but are often abused. "Per minute" stats are irrelevant in terms of extrapolation; a player who produces a certain amount in 8 minutes is *not* likely to produce five times that level in 40 minutes. However, I think they are fairly useful in comparing players of fairly equal numbers, to put them on a level playing field. For instance, if you want a quick and easy way to compare one player who played 30 mpg, and another who played 34 mpg, looking at their "per 36" or "per 48" numbers are a fairly decent way to determine who had better stats.
I'm not really a fan of "+/-", because I think these stats are overly reliant upon: 1) the teammates a player is playing with, and 2) game situation (ie, do the bulk of minutes come against starters or in garbage time). I know some members think that this stat proved that Rajon Rondo is the best player in the history of the universe, but to me, it's not a great indicator taken out of context.
It's the same thing with Opponent's PER: this stat alone isn't a great indicator of a player's individual defense, because players who play in an up tempo system are going to get killed by it. If an opposing small forward is constantly scoring points against your team on the fast break, does that mean that your small forward is a horrible defender? No -- it means that your team gives up a lot of easy hoops due to its system.
One new age stat I really like is eFG%. A lot of players have a lower overall FG% because they take a lot of three pointers; this levels that playing field, and shows who the truly great shooters are.
I of course use all of these stats from time to time (except the completely and utterly useless WP48). However, it's important to note that you have to use them in context, rather than manipulating them to win an argument.