Early on, I do the same thing as Garfunkel. I have a dedicated fast transport for single units to ferry them to new worlds. Once I get HQ units up, then I have a dedicated Brigade transport for moving brigades between worlds. Its a commercial engine design, as I found that the be the most economical way of shuffling units from the homeworld to colonies.
For actual assault units;
Early on, I go for military engine brigade transports with heavy armor, heavy shields, and anti-missile turrets. They are fairly cheap, and they can get the troops down without worrying about losing a whole division if they take a hit. Also, especially early on, it doesnt take very many brigades to hold/capture a world. As the tech levels increase, so do the troop costs.
I build big division transports when cryo and drop modules show up. I only use cryo for bulk transports, not for combat drops. If I use big combat transports, I usually stick with the heavy defense scheme, and size it up to a division.
One thing that does work quite well are LST type ships using FAC troop transports and drop modules. I load the troops from the big transport to the FACs, then send them in. It works pretty well. Where the LSTs really shine, is in seizing all the mining/outpost/listening post locations in systems. You can get a lot of troops all going in different directions, and do it fast. Helps a ton when you grab a big system.
