These come from a variety of genres, but they all have conclusive endings.
Bakeneko
Bartender
Cross Game
Dennou Coil
Kemono no Sou-ja Erin
Ghost Hound
Saraiya Goyou ("House of Five Leaves")
Seirei no Moribito
Mononoke (anthology series; each arc has an ending)
Monster
Mouryou no Hako (search Google)
Nodame Cantabile (if you include the sequels)
Noein
Oh! Edo Rocket
Planetes
Saiunkoku Monogatari (Out-of-print. There's a second season, but the first does conclude.)
Shion no Ou
Tokyo Magnitude 8.0 (just
licensed)
Tsuritama
Usagi Drop
Juuni Kokki ("Twelve Kingdoms") has a decisive conclusion to the main arc which covers episodes 1-39. There's a second, six-episode story which is very rushed because the novelist became ill.