I use Time Adjuster which comes stock in Pro Tools, and just picked up UAD's plug version of the Little Labs IBP.
Side note: I would have never paid the 100 dollar price for the IBP, but I had a coupon that made it only $25.
I'm not familiar with the Auto Align...
*edit* I just checked both auto and mautoalign, they seem similar in function, but mautoalign is less than half the price :O
I use Drumatom and that is great but it doesn't do what the SoundRadix does for phase. I tested out the SoundRadix once and it is really a great tool, but it's as much of a workflow tool as it is anything else. One could probably achieve the same results by very carefully analyzing the phase relationships between all your drums, aligning them properly and flipping the phase when necessary - but who wants to spend all that time doing that when there is a quick fix in a plugin. I may buy it eventually.