45 minutes is just enough to help a bit with overall aerobic conditioning. If you're doing this every weekday, plus doing longer rides on weekends, you have enough time to work with to train for pretty much anything except ultra events. My suggestion would be: Early in your season, don't worry about intervals, just keep your heart rate pretty low. If you get bored, try some days of spinning in a lighter gear than usual (concentrating on a smooth cadence) and some days in a slightly harder gear than usual, to work on leg strength. A fixie is also good, but not in the early season if you're doing hills, because your heart rate will go too high.
If you're starting off with 3 hour rides once a weekend, you're getting a total of just under 7 hours/week. Build that up, at 10% - 20% per week, by doing longer weekend rides. Try not to ride every day - you progress faster if you have at least one day of complete recovery per week. For people who don't get burned out and want to ride every day, some coaches recommend a 4-week cycle, with one easy week with at least 2 rest days after three weeks of training.
How much you need to build your aerobic base depends on the kind of events you're training for. If you're looking to do 50 mile rides, just build up to the point where you're doing 50s on weekends. If you want to do centuries, build up to about 75 on weekends.
Once you've reached that point, you can start adding intervals. A good approach is to start with two 10 minute periods of elevated heart rate. Start with 20 minutes of warm up, then accelerate to the point where your breathing is hard enough so that you can talk but not sing. It should feel slightly uncomfortable. Ride very slow for 5 minutes to recover in between, and try to get 5 minutes of cool down afterwards. Ideally, you would build these up to 3 20-minute intervals, but you don't have enough time on your weekday rides. Do this no more than twice a week. The trick is to find a point in your ride where you can do the interval without stopping for lights etc.
After 3-4 weeks like that, go to sharper intervals -- warm up, 5 minutes on at a maximum pace, 5 minutes recovery, then cool down. Start with 2 reps, and build up to four or five. Again, don't do this more than 2 times a week. After a couple weeks, start mixing in other types of intervals, like the ILTs mentioned by someone above, or stomps, depending on particular areas you want to improve.
Good luck.