We used FantasyAuctioneer last year and it went pretty good. 12 teams and 25 man-rostor. took a little over 3 hours to do. it moves a very quick pace so there isn't much time for you analyse draft sheets, etc. We are definitely going to use it again this year.
as for sites, I can only comment on the 3 i used last year.
yahoo. great site, but doesn't handle many of details for keeper leagues, ie. salaries, minors
cbs. loved this one the most for keeper leagues. only negative is it doesn't support FAAB. supports salaries, minors, and keepers
tqstat. absolutely hated this the most. only positive is that it supports FAAB. UI is crap. biggest grip is that it doesn't have email notifications for trade offers, etc.