I plan to start working out my lower body once a week in the gym as well as commuting to school 2-3 times a week (38 mile RT). For you guys who do this and ride your bike regularly, when do you do lower body workouts so it doesn't affect your cycling?

They always affect your cycling. You can't get something for nothing. If I do them at all, I do them after cycling, so they don't impact my rest days.

Carbonfiberboy is right: lifting will affect your cycling. For me, lifting once a week is easy to fit in, and twice can be done with planning, but 3x a week and trying to ride high volumes is difficult. This is why most guys only do once a week during the season, if at all. I think once a week is a good plan to preserve your gains from the offseason, but you might not gain much.

It would be best, in terms of getting the full benefits of each workout, to lift and ride on separate days. There are only so many days in the week, though, and you need one or two off.

Honestly, I feel like a beast on the bike after I lift, so I have no problem doing a fairly intense, but shorter, ride later in the day. I wouldn't do Tabata intervals or anything, but an hour-long, fast-paced ride feels good to me. Anything over that and the caloric demands of cycling, and the slow in protein synthesis during exercise are probably going to be to much to allow you to recover well from the lifting. What you can do depends on you, of course. This just seems to be my limit.

My suggestion to you would to keep your goals separate here when you are lifting and riding on the same day. That is: work for strength and power in the gym, and save the intense cardio for later; basically, take your rest between sets, don't worry about supersetting, and don't try to kill yourself in the gym. All of these things can be fine (although you really don't have to brutalize yourself to get results), but they are what will interfere with your riding the most.

Other than that, you just have to watch your nutrition closely.

I would lift and then ride to get the full benefits of the lifting workout. Would you ride for 2 hours and then do your most intense interval workout? I wouldn't, because I wouldn't be able to really work during the intense portion of the workout, and wouldn't be able to get the benefits of doing it.

I'm the complete opposite. I do lowerbody weights before each ride. Once I've built up my strength in the weight room, I can bring my new strength and movement patterns out on to the bike at a higher velocity, lower load exercise = (Power) which is the cycling & start doing interval training (Stomps). I feel much stronger on the bike having done weights prior, its all about controlling the intensity & adapting, you make the workout as easy or as fatiguing as you like, finding the right balance will be key. I'm after developing power for my own circumstances, so that comes last.

This is where I'm at. But...

there needs to be a speed element to create great power. My lifting is mainly heavy & slow (strength), with some explosive movements (Dumbell Jump Squats) but power has to be created elsewhere for me.