In Coimbra I usually recommend the Hotel Victoria.
I have stayed there several times and Dona Rosa and Sr. Leopoldo are great!
There is a new wing which opened 18 months ago.. The in-house restaurant offers good food as well.
It does not have the quaint location of other hostelries but at the Victoria there is a parking garage(paid) 1 block away.
The good thing about the Victoria is that it is on the edge of the (pedestrianised) old Town and in easy walking distance of the Old Centre, the Old University area and the riverside, There are also several restaurants in the area as well.
In Coimbra, I would also recommend visiting "Fado do Centro" to get a taste of the famous student music style of this City.
Some more info here: http://bit.ly/18k4zuf