Boat Shoes # 1, from "Ki'I's Don't Lie"

Boat Shoes # 1, seen again in "Flashback"

These were primarily used during the early seasons and the last episode I can recall seeing them in is season five's "Mac's Back". They are also the only ones I can make a positive ID on. They are Sperry Top-Siders, and I think the particular model is called "Sea Mate". As it is Sperry recently made a limited re-issue of this shoe for their 75 anniversary. They are available at L.L. Bean for $44.
http://www.llbean.com/llbeansignature/l ... at4=505905
Boat Shoes # 2, seen here in episode "Compulsion"

This second pair is probably TM's most frequently used shoes. Brand and model are unknown to me. There is no external branding from what I can tell.
Although I'm not 100% sure, it's probable that "boat shoes # 2" are Sperry Top-Siders. The material either-way seems to be rough-side-out leather or suede. As part of Sperry's 75th anniversary range, a pair damn near identical to these are also available. RRP seems to be $90.
http://www.sperrytopsider.com/store/Sit ... cat90046DM
Boat Shoes # 3, taken from "Thank Heaven For Little Girls and Big Ones Too"

These brown leather boat shoes are probably the most rarely seen of the three. The only other episode I can recall seeing them in is "Going Home".