I always use the stratagy of big, expensive, quick ships. They take a while to build, and are only worth building on a few key industrial planets (due to the time involved). I usually will have certain planets that I will rally the fleets to, then have the fleet cover between two to four star systems (which is why speed is neccesary) along my empires perimiter.
I figure that the best defense is a good offense, so even if I am not attacking, I use the fleets to intercept anything coming in before they reach my planets.
I usually play on gigantic galaxies, with rare stars (tight clusters), and aboundent on eveything else (it gives it a big empty space feel), so I don't have a whole lot of planets initially to maintain huge numbers of ships (if I have a hundred ships then I am usually stretching my economic limit). So, the smaller fleets are good for my economy.
The size of ships that I use are:
Tiny- At the startup, they are cheap and quick.
Medium- My next step up from tiny, form my intial backbone, and it is here that my fleet stratagy really begins to come into play.
Huge/Massive- Once I have this I stop building mediums and switch over.