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.