RIght now I use a fairly complex spread sheet that calculates everything based only miles flown and fare code. It's very AA specific, but it calculates...

Q-Points
Q-Miles
Actual miles flown
COS bonuses
Elite status by segments and miles
Miles(YTD, Actual Total,Lifetime)
Cost YTD
Million Miler status

I've developed one for HP, BA, VS, Hilton, and Starwood as well.

I'm still developing a web based DB that will encompass all of this info so I won't need seperate spreadsheets.