Well, the trick is going to be applying pressure to whatever substance you want in order to force the balloon to expand.
I imagine if you took a soda bottle, filled it with the substance you'd like, put the balloon over the neck of the bottle and then applied pressure to the bottle, you could probably fill the balloon like that.
Having a funnel will probably help with filling the bottle.
In this thread https://umd.net/forums/water_balloons Gunging mad Rugby says he uses "a garden sprayer (under pressure)". A few posts down Silver_sea gives a checklist for using a bottle. If these methods are ineffective or impractical, maybe the latter method can be improved upon. As abgamma points out, pressure is key. If you can puncture the bottom of a plastic bottle with an air pump needle (like for basketballs -- hopefully a hammer would do the job, and maybe using a skinny nail first), then a bicycle pump could be attached and used to increase the air pressure inside forcing the gunge out of the opening at the top. Might save the trouble of squeezing a bunch of plastic bottles by hand anyway.
1. put mess in a soda bottle 2. blow up balloon to the size you want 3. While still pinching the balloon at the neck, place the balloon openning on the soda bottle. 4. Flip soda bottle/balloon upside down, while holding onto the balloon so it doesn't fall off. Mess is more dense than air so it will fill the balloon.