Quarry Lakes is the main spot to fish in Fremont. There are 2 lakes here. Horseshoe lake has trout, a small population of smallmouth bass, catfish, carp and bluegill. Rainbow lake just has largemouth and catfish. The fishing over there is usually hit or miss (mostly miss). Although I have had my some good days. I once caught 10 trout in 1 hour over there off of different spoons and kastmasters. Chartreuse powerbait and a night crawler work well too. The catfish bite off of chicken liver is pretty decent too. In Horseshoe, try to the left of the swim beach, or the main point on the peninsula. Never had much luck off the dock. Fisherman's Row ( to the right of the boat launch) is not a bad spot either. Kind of shallow though, but the further you walk down the deeper the water will get. In Rainbow Lake, senkos or just a plain old night crawler will catch you some bass. The good thing about Quarry is that it's a good place to fish in the rainy months because the water doesn't get muddy.
You guys should definitely make a trip to Del Valle sometime. A great spot for cats is off the rocks by the marina. We used to toss chicken liver there after work, and with in 5 minutes we would have a cat. I almost got tired of catchin them, it was so easy. It's also probably the best place for trout in the bay area. I've lost count of how many limits i've caught there. The night crawler/ white power eggs combo is a great standby, but most of my trout have come off lures like Kastmasters, spoons, inline spinners, or crankbaits. It also has a decent bluegill and crappie population, and as an added bonus there are some huge stripers in here. It gets water pumper in from the Delta so any fish that's in there can be in Del Valle. I've also seen some 50" sturgeon pulled out of here, but those are rare.
I've been hitting up Anderson Lake a lot lately. Not at the dam entrance though, go to where the bridge is off of East Dunn Ave. On hot days the bass will chill under the shade of the bridge and you can catch them from shore. Lake Del Valle is also a decent lake for bass. I used to work there and i've seen some huge ones pulled out of there. It's also great for trout and the catfish bite is pretty damn good right now. Shadow Cliffs is not bad either.
almaden lake (for bass) is the spot i hit up because it is close to my house. but if you are going to eat the fish you wouldn't want to fish there because they are contaminated with mercury. another good lake (bass, bluegill, and catfish) if you have a boat is anderson dam in morgan hill. i will also hit up the campbell perc ponds after the kids fish weekend. you can pull out some good size trout.