In Tofino, Schooner or Sea Shanty both have very good seafood (Schooner has a more sophisticated menu and wine list), Sea Shanty has a better view! Tofino Chamber of Commerce web site has a restaurant section and some links will have menu information.

http://www.island.net/~tofino/

The best fine-dining in the area is probably the Pointe at Wickaninnish Inn (near Tofino). Beautiful location, sophisticated and inventive menu and wine list featuring West Coast items. A real winner.
http://www.wickinn.com/

The Tin-Wis hotel has a restaurant with native Indian items, but we found the service there pretty poor.

In Victoria, there are many, many good restaurants. Cafe Brio does have a Tuscan influence on their menu but they feature local items. Highly recommended, but no view. Menu at:

http://www.cafe-brio.com/

Pescatores Fish House does seafood in innovative and classic ways...

http://www.pescatores.com/

Milestone's (on the Inner Harbour) has one of the best locations in the city. Get a booth by the huge windows (open to let the seabreeze in) and look out over the harbour and the Empress Hotel. Stay until sunset and watch the Legislature building get lit up with thousands of lights. Very comfortable seating, mixed menu, good quality. No web site!

Sooke Harbour House and the Aerie Resort are famous for their menus and winelists, but are further out of the downtown area. You would have to drive to them, but it might be worth it if you want something really special.

For casual fare, Spinnaker's Brew pub, Swan's Brew pub, the Harbour Canoe Club and SouthBay all have excellent locations on the water and nice views. Menus vary and can be quite tasty, as are some of the local beers.

One of my favourite spots in the city is the BlackFish Cafe (on the Innner Harbour, where the floatplanes take off and land). It is a small casual cafe but I love to sit on the floating patio (on the water) and sip a BC dry sparkling apple cider and watch the floatplanes come and go...