You can make the classic transformers sound using a flange and tremelo and preferably source input that rises and falls in some way.
For example ....choose anything from a simple sine to a complex sample, slow lfo on it's pitch, pass it through meta flanger into tremelo and fiddle with the trem speed etc.
For more complex transformations, it's good to choose your source samples wisely.
You want a disparate mix of machinery,various automobiles ,metal being played with, all at varying lengths ...then some pre-rendered synthesised source fx such as filtered noise , laser zaps, dark menacing tones, sub elements.
Obviously all source should be well recorded. Don't use anything that can't be warped without losing it's quality too much.
The you can go about combining these in various ways. This depends on what software you use....
As said above, synths like Massive and Dcam are good for creating your synthesised parts.
Alchemy is great for combining and manipulating your source. Reaktor is always handy for both.Using Kore fx is ok also, especially if you modulate the fx paramters using same controller/envelope change affecting the sources envelope(s).
Generally speaking,you want to experiment with the pitch, speed, direction, frequency of each sample. So set up envelopes for those parameters on your sampler or record automation to reuse. Trigger the samples manually in different orders ,or several together. You'll start to modulate the envelopes of each to work with the other and the sounds will then start to mould together.
An easy way of doing this is to use multiple channels in your daw,
Example, loading your chosen sampler on three channels.
In each , assigning a different range of source samples and modulation settings, then triggering all three by keyboard note,you can delay or change note on separate channels to create different combinations.
Render these as you are manipulating them.
Now you have a whole variety of organic machinelike modulations
Then you lay these out on another sampler to trigger, manipulate and combine them in sync with your project.
I made a similar library called robostep, which can be found here