I see this thread is a bit old but thought I'd bump for interest.
I've been weight lifting on and off since 07. I was diagnosed in 04 I think. My gains have of course always been limited since for an average person gains are probably 50/50 diet/routine, when you start, you'll make gains pretty much no matter what, as you progress your diet becomes more important, and at an elite level it probably goes back to 50/50 again, where diet is super important but so is routine.
As a CD patient you're probably looking at 90/10 diet/routine, or close to it.
If you have chronic diarrhea, like I did, you probably won't see much gains because you aren't digesting food right. If you have motility issues or anything like that you're going to struggle to gain weight because you're just not getting the calories you need.
That said there's a lot to learn and it's hard to learn when all the advice is geared toward normal, healthy individuals, or steroid users, I can never get a straight answer on bodybuilders.com half the time except 'ask your doctor' so I've had to learn most of this myself.
What I've gathered so far is this:
-Find a routine with a MODERATE intensity, that you can attack each day well rested. Soreness afterwards is perfectly acceptable, soreness the day of your next workout is perfectly acceptable. Fatigue however is not and is symptomatic of over-training and as a CD patient you are more prone to this. Listen to your body should be your rule of thumb here!
-Whatever anyone tries to tell you about a magic number of reps, or sets, is entirely subjective and personal, you have to do what feels right for you.
I highly suggest this guy's Youtube videos
http://www.youtube.com/watch?v=7TBr8S8FZdE&feature=share&list=UU0ASolYU_Yh3yShLFQC0stg
I just found him, and he is unlike most Youtube health gurus who are one-approach nazi's for their preference. He explains options, and tells you why one does one thing better than the other, but more importantly he understands bio-mechanics, and building a body with -healthy- strength, not just aesthetic size, as well as the mentality and life philosophy behind everything, he's very down-to-earth.
Some of his titles may be sensationalist to draw in views but you'll find the information very reliable.
I also like that he advocates Paleo diet, and all workout routines, whether it's crossfit, bodybuilding or strength training, he doesn't tell you anything is best, it depends on your goals which is 100% true.
http://www.exrx.net/Lists/Directory.html
This is a good reference websites for muscles, workouts that stimulate them and proper form.
http://forum.bodybuilding.com/showthread.php?t=121353501
I highly recommend this as an 'intro' routine for CD because it's balanced in intensity and rest.
The short version is you rest and workout every-other day and you're doing squat-press-deadlift-row, or some variation of this. This means you hit the same body part once every 8 days, so you're never over-worked and fatigued. If you feel this becomes too 'easy' and think you can up the intensity, you can find a faster paced one in the future.
Early this year when oils started to disagree with me I got very sick and lost weight, down to 110 lb.s (5'11.75") I'm back up to 129 in a few months with a fairly low cal diet and some proper exercise and I have to say it shows, I used to hover at 114 when healthy and not exercising.
I follow the routine I linked but have increased the intensity for my personal tastes.
I do squats & abs - rest - back, biceps, tricps - rest - deadlift, traps & abs - rest - chest, tris, bis, delts - rest - repeat.
It's nice because you don't have boring luls on weekends where you do nothing for 2 days, but also you're never drained.