Well I can tell ya one thing I'm happy I found out about- Amon_RA and CWM nandroid images are NOT cross compatible. If you have a solid nandroid you made in CWM, don't restore it in Amon_RA. I was so close to doing that 'til I found a thread on it a week ago or so...
I can't really help with too much, but one thing I noticed that killed my phone's stability was restoring too much with Titanium Backup. HTC's Sense-only programs and widgets may try to start in CM7 on booting up and can cause all sorts of hell, as does restoring data from Sense-based ROMs. I learned that the hard way! It's a pain, but it's essentially why I've made CM7 (AOSP) my main ROM. Messing around with Sense isn't worth it to me, given the incompatibility with my preferred ROM.
---
I'm no expert with Titanium Backup by any means, but if I were to go to a new ROM, I would batch restore almost all apps without data, except for ones that are architecture-specific, to AOSP or Sense or whatever. Then batch restore data, but only select ones that I need it for... Titanium Backup is complicated and I'm sure others can provide more helpful info, I try not to rely on it too much! Somehow, I've lost my market links for the majority of my apps in the past week, and TB could only restore a small amount of them. I have no clue what to do about it, haha.