There are 1926 pages on Teaspoon, 864 of them for the current 10th Doctor era alone, each with about 20 stories. Use the Search function to look for what you want. You can search by pairing. genre, rating etc. What kind of stories do you like? There are LJ communities like DW_Femslash, Who_OTP, Girl Reporter (for Sarah-Jane Smith fic), LifeonMartha (Martha Jones-related)... I tend to go for well written femslash with a good plot and reason for two characters to be together.
AFF.N does have a lot of Doctor/Jack and not much else, which is why I posted one of mine here ([PLUG]The Bermuda Triangle, first one on the list on here although it's a pairing that may freak you out[/PLUG]), as I tend to like longer stories with "the whole 9 yards" too. If the characters aren't well written and true to their TV selves - no matter how strange the pairing or circumstances may be - then you may as well be reading an original fic with original characters. Doctor Who is one of those formats that can sustain any kind of story or situation without violating its central tenets.