It's pretty decent. Worse when flying on a partner of the program you're crediting. A few anecdotal datapoints:

1. LAN Airlines (oneworld). I started accumulating all my AA trips (which are only about 15% of my total flights) because I was also taking a LAN Argentina domestic flight in a cheap fare class that didn't count for AAdvantage. Figured since my AA account was empty/no-status I'd credit to LAN in 2006-07 to get some reward. AA is annoying just like DL in this way: there's no way online to put in a partner FF# - you always have to call, or else do it at check-in or gate. The one time I actually saw the LA# print on my AA BP is the only time the flight didn't get credited to LANPass.

So about 25% of my AA/oneworld flying or about 4% of my overall flying didn't credit.

2. Delta crediting to NW. Happens 100% of the time faster than NW itself, if I can get India to understand me when I call to give them my WorldPerks#.

3. UA - lost 867 miles on a DEN-BOS that became a DEN-ORD divert with a next-day ORD-BOS. By the time I realized I'd never gotten it, it was over a year old (I was less miles-obsessive in 2005). Never had UA miles fail to post except in this situation where I think they de-boarded everyone from DEN-BOS when they rebooked people instead of doing it the right way.

Overall I've been pretty lucky in getting flight miles to post about 95% or better, as long as I do my part of extra verification when flying partner metal. For example I'm flying to Munich on a UA-ticket, UA-fare, UA-codeshare/LH metal outbound with a LH return TATL leg. LH didn't have the UA MP# in their locator so I'm sure I would not have gotten miles automatically. I got the LH locator from UA, then used the customer service form on LH's site to request adding the MP#, then verified it showed up on checkmytrip.com after they entered it.

Partners whom you have to call, and irrops. That's pretty much the only problems. Getting the "home" airline's flights to post usually works 100%.

Hotel miles usually show up, but HHonors has messed up posting to LAN a couple of times.

National has messed up rental car miles to NW and to UA a couple of times. Maybe about 10% don't post, or post as base miles without promo coupon credits. Hertz is better in this area. No way I'm ever renting again from Thrifty/Dollar so I don't know about them.

NW Mall is slow and sometimes inaccurate. I use drugstore.com a lot and one of the annoyances with NWA Mall is that each line-item in the order posts separately, at a different time. So I might order well over $50 of stuff which might qualify for some NW promo, but it posts as $3 for a bottle of Tylenol, $2 for deodorant, etc., instead of the order amount. Then I have to call or email NW.