When I was first picking up the basic rudiments of guitar playing, a friend told me that there were certain chords where you need to use your thumb. One of these was the D chord, which he showed me as 200232 - before, I'd only known it as xx0232. Another thing he showed me was how to make barre chords more easily - by using my thumb to fret the bottom two strings for an A-shaped barre and the bottom string for an E-shaped barre. If I'm playing a 12-bar blues around the 5th fret, I'll start with full barres - but if I'm playing open chords and wish to switch to a barre, I'll probably use my thumb - I find it quicker, and with the added bonus (for me, I don't know about anyone else?) that it automatically seems to put my other fingers in somewhere approximating the correct places.
I do have large hands - maybe this wouldn't work for someone with small hands, but for me it's always worked fine - and it's good to have both options.
I'd say put your thumb where it's most comfortable for you - with time, and practise, you'll come to think of it as a natural 5th fretting finger instead of just something to hold your guitar with.
Vic