I have been wondering if and how the Imperium would transport non-warpdrive equipped vessels (aka system ships) between different star systems.

The' if' seems easy enough to solve: it would make a lot of sense. If you start to exploit a new system, larger system ships are vital and you can hardly wait till you have created the necessary industrial facilities (planet bound or even orbital) to build them. On the other hand, keeping the dedicated warp capable ships around to do this jobs seems a waste. And keeping Navis Nobilite on them even more! Furthermore, the Imperium is capable of transporting Ramilies class fortresses, so they have the technology.

Which brings us to the how, some thoughts crop up:

- Ships might be towed. In which case they would need a proper gellar field to protect them from the dangers of the warp. Furthermore, this seems risky as hell. But it can be done.

- Another possibility might be a Cetaceus like transport that gets smaller ships from one system to another (just like some real world ships). This seems an elegant if expensive solution, and would give a highly searched for ship to aid colonization attempts.

Have any of you had any experience in your games with this? Any thoughts?

System ships can be rather small. The most expedient solution would be to lash them to the hull of whatever freighter is heading that way and extend the gellar field around them.

If you're ship is too big to tow just pull some of the divider walls on a universe class. What was that one guy saying? Carries like forty Nimitz class carriers per bay and has some ungodly number of bays?

I highly doubt they have a ship devoted to it. New systems are sort of rare in places they have monotask hulls devoted to anything. I might be interested in the idea of a hire out vessel from the mechanicus that does nothing but fly around and make simple stations, ships and bases from local materials.

They sure can, especially in a binary or trinary star system!

The interesting thing you have noted is the "Without a warp drive" feature. There are Chartist captains, who are Imperium traders without Navigators, who still possess a Warp drive. They make very brief, micro-warp jumps that allow them to travel between systems at a speed of roughly 1/5th that of a Navigator-assisted jump, but on the other hand are actually much more reliable in terms of time of arrival. This is the same method that the Tau use, and these ships are usually exclusively transports. They're also mentioned as being smaller, which might be because they are just smaller vessels, or the Gellar Field might just take up a lot of room inside of the ship

I do allow for towing in the warp, but the ship being towed must be much smaller than the tower.

If you read in the stuff for Fleet Base Metis, they describe how a Mechanicus fleet towed the mighty Ramillies through the Warp, to its current spot, nearby the Jericho-Maw Warp Gate; it was only when they realized that the star fort couldn't survive the trip through the warp gate that a lot of people got summarily executed, and they decided to leave it there, and monitor the gate from this side; sort of a last line of defense if anything hostile got through the Jericho side's gate. Thus, if you can't do it like the Tau, and hook the ship to your hull, you can tractor/tow it through the warp, either on HUGE chains (seems silly, huh, but totally something they've done), or some sort of archeotech tractor beams. I imagine this is among the most terrifying, harrowing experiences, since those ships are depending on their tows, and not accustomed to, or even possessing of, a Gellar field, but it is certainly possible.

A Ramillies has got a gellar field if I remember the fluff correctly. But it is obviously totally dependent on its tows to move it about, so indeed, extremely harrowing.

So on a smaller scale, getting a few system defence monitors from system A to system B should be feasible, either by being carried piggy back or towed - in which case they need a gellar field.

Priests of mars has a ginormous mechanicus explorator spaceship that can store smaller ships inside.

Indeed. Provided you've got access to something which can carry it 'inside' I'd say it is fine. If not....you can in theory hold station inside the Gellar Field of another ship (towing cables or just station-keeping with engines) but obviously that's quite risky because if you lose your position you're dead. Hope the navigator and helmsman don't screw up their rolls, and keep the PCs on the starship!