Is there a way to transport ships without repackaging them in Eve online?

Flying them there manually is an option for some ships, especially if it it only one smaller ship. In lowsec it is usually enough to fill the low slots with warp core stabilizers and most gate camps won't be able to catch you. I would not try this with a battleship, but it works very well with cruisers.

If you have access to a carrier, they can transport 1 million cubic meters of fitted ships. This of course only works outside of highsec.

Theoretically someone in a Titan could bridge you to your destination if it is inside range, but that is likely not a practical solution and would also only work for one ship at once.

As far as I know freighters can also transport fitted ships if you put them inside a courier contract package. Fitted ships are rather large, and you will only be able to transport something like 3 battlecruisers or 9-10 cruisers that way. If you don't mind paying then you could just contract your ships to Red Frog and let them transport them to your destination. This only works in high-sec, in low-sec and null-sec you would use jump freighters with lower capacity and much higher costs.

A new ship has been added. It's bigger than the Orca and can transport ships packaged (dec 9th patch): The Bowhead.

A.) Pay someone for a courier contract to move them.

B.) If you have the skill get a bowhead and move them all at once.

C.) Fly the ships and go back in a pod/shuttle.

Another option for high sec only would be an Orca. Much easier to skill into and use compared to a freighter or carrier, less expensive at 600M for just the hull. They have a 400,000 m3 ship hanger for unpackaged ships which is 8-12 cruisers or ~2 battleships. They can be tankier than a freighter when fit correctly (200k+ ehp) and align faster than a freighter. Preferably use an alt with it, especially if you have active wardecs.

I've seen people cart them around low sec, using a webbing alt and scout. Whether you want to take that risk is up to you. I imagine in null sec, it would die at the first bubble.