I own a 29-2 and my friend just got an anaconda. They are both good overall but here are the differences that I observe:
1) The colt has the typical colt DA pull. But if I remember correctly, it was better than most colts, in this regard, that I have handled/shot. The 29-2 has a pleasant, even throughout (no stacking ie increased pull before trigger break), DA pull.
2) The anaconda has a full lug where my 29-2 does not. This makes the anaconda slightly heavier which is good for a 44 magnum. Some 629s and a few 29s (magna classics) have a full lug as well. IIRC every anaconda has this feature however.
3) Almost any colt revolver, due to the frame angles/design, sits lower in your hand than a comparable S&W. While this doesn't factor in much for 2 hand shooting, for 1 hand, I think its more comfortable and easier to shoot.
4) I don't recall the anaconda having any kind of a special trigger or hammer but my 29-2 has the TT and TH. I prefer the wideness of the TT and TH but thats largely personal.
The colt rotates clockwise, S&W rotates counter clockwise and both have excellent SA pulls. Aside from durability issues with anacondas, I'd say its a tie overall. I shot my friends anaconda that day just as well as my 29-2.