Disclaimer: There is not one "best answer" on how to apply compounds. It can depend on what compounds you get early, what your agents already have on them, what you want to achieve etc. You can put whatever you want on them, then remove everything and start over again, the time and money cost are very low compared to moving and upgrading.

I also want to thank everyone who helped me on this guide, pointing out errors, suggesting other build paths, giving feedback etc. Thank you!

In this guide, I will list all the known substances you can enhance your agents with.
Every compound can need one (or no) compound to be present on your agent to be applied and can block one or two other compounds, which can not be applied after this one. (Note you can still do it before!)

There are 7 compounds that can be applied without requirement:
AMPEA, DXAMPEA, TST, BMA, THG, Bolasterone and Gonadorelin.
I will refer to these as "chain starters". Every compound is part of exactly one chain and will block compounds of other chains, not necessarily starters.
Every compound in every chain relies only on the one above (and by extension, all compounds above that one). When a compound is blocked, I have not only given the compound, but also the chain where to find it.

It seems like every chain splits up after some time: Two compounds from one chain rely on the same compound. Sometimes you need to apply one first, sometimes it does not matter as they do not block each other.

For values, I will list the cumultative value of the chain up to this point.
Example: AMPEA gives 14 / 7 / 5 / 8 to Circulatory, Sensory, Respiratory and Motoric respectively.
EPO, depending on AMPEA, gives 13 / 0 / 0 / -2, but I will list it as 27 / 7 / 5 / 6 as you need to have AMPEA applied.

I have not verified every single value by myself, and I rely on Yograins guide "Body Engineering" for the values. If any value is wrong or has been updated, please comment.

Note: Ralixofene and XENOXY both depend on ARGOXY. For this guide I assumed you applied ARGOXY first. It is possible to apply Ralixofene first, at it will not block ARGOXY.

Keep in mind that you will get values subtracted when applying Ralixofene and AMPK, but will get them back with Albumin.

ARGOXY will lock you out of the DXAMPEA-Chain. However, you only lose 28 total value for 171 that you still can get in this chain.
The best option here is probably to go for this chain, and take what you can still get from DXAMPEA.

Note: Both Mannitol and Formebolone depend on Danazol. It does not matter which one you apply first, as they do not block each other. For this guide I assumed you apply Mannitol first.

Applying this before the AMPEA-Chain locks you out of the best part of it. My advice is to apply it after AMPEA, giving up Formebolone and Stanozolol.

Note: Calusterone and Cyclofenil both depend on Bolandiol. It is advised to apply them in this order, as Calusterone blocks Cyclofenil.

Be sure to apply this chain only if you have all compounds available. When you only use Bolasterone and Bolandiol, you will get negative values for Circulatory and Motoric in exchange for 19 sensory. You might also lock yourself out of Cyclofenil if you use Calusterone too early.

Apply after TST, but before AMPEA, as it would lock Calusterone.
This chain also locks Gonadorelin-2 and -3, but you don't want these anyway.

Two options here:
1) You can apply this after your DXAMPEA-Chain, so you don't lock Mannitol (DXAMPEA-3) but before AMPEA, so you don't lock this chain.
This cuts off you AMPEA-Chain at ARGOXY (AMPEA-3).

2) Apply TST, the AMPEA-Chain and the DXAMPEA-Chain until Mannitol. Then you can apply Anadrol to avoid locking Mannitol.

Not sure if you can call this a "chain" at this point. This blocks compounds from the AMPEA-Chain, but is blocked by EPO (AMPEA-2). Drop it, as following the AMPEA-Chain gives way more value.

These two compounds block other compounds from the DXAMPEA-Chain. DHEA and Formebolone block each other, so you apply the DXAMPEA-Chain until Mannitol, then BMA and DHEA.
DHEA gives more overall value than Formebolone and Stanozolol combined, you can swap it if you are missing DHEA or want to focus on Respiratory.

Also note that AMPK blocks BMA and vice versa. You have to choose between BMA and the end of the AMPEA-Chain.

Only 40 total value. Not very useful to focus on, but you can try to sneak just the first one in.
However, you want to keep at least Ralixofene and AMPK (AMPEA-5 and AMPEA-6) open, and probably Anadrol too.

First order: Best overall agent, total value of 498
It is recommended to use this when you have an agent with 61+ base circulatory.
Combined with the +139 Circulatory, +126 Sensory, +130 Respiratory and +103 Motoric from these drugs you get over 200 Circulatory, which leaves you with 4 AP and 3 FP.

The Idea here is to follow the AMPEA-Chain, as it gives the highest total values. Add what you can get from Bolasterone and mix in everything that does not lock you out of important stuff.
Will be applied later - Already applied - Not used


Reasoning:
Full AMPEA-Chain:
AMPEA, EPO, ARGOXY, XENOXY, Ralixofene, AMPK, Albumin, IGF-1

Almost-Full DXAMPEA-Chain after Albumin as DXAMPEA blocks Albumin
DXAMPEA, Danazol, Mannitol

Almost-Full Bolasterone-Chain, can be placed anywhere
Bolasterone, Bolaniol, Cyclofenil

Now squeeze in TST anywhere before Albumin and Anadrol behind TST, but before Cyclofenil.

Second order: Maxing out on weaker agents
With +149 Circulatory, +130 Respiratory, +109 Sensory, +91 Motoric this order gives less overall stats ( = 479 total), but focuses on Circulatory to get every agent to 4 AP and 3 FP.
You need only 51 base Circulatory, which every late game agent should have.

The Idea here is to cut of the AMPEA-Chain early, which locks us out of ARGOXY and the following compounds, but enables us to get THG, TST, Anadrol, BMA and DHEA.


Will be applied later - Already applied - Not used

Reasoning:
We use the beginning of 5 different chains, most of them are independent from others and there is no need to cross between chains to prevent lockouts. This makes this one easy to apply, because it is not as complicated as the other order.
You still need to watch out for some parts in this order, other than that you are free to move them around based on what you have:

THG
AMPEA, EPO after THG
DXAMPEA, Danazol, Mannitol
TST, Anadrol after Mannitol
BMA (after Danazol), DHEA
Bolasterone, Bolandiol, Cyclofenil after Anadrol.

02.09.18
Took some time to update, but now I am back ;)
- Added values to the 498 total order
- Added another order which focuses on Circulatory, boosting you to 4 AP and 3 FP.
- Minor fix: Added BMA blocking AMPK
- Minor fixes: Spelling and punctuation ;)

26.8.18
- Added an order which gives +498 total.
- Added IGF-1

25.8.18
- Added Stanozolol, Calusterone, XENOXY and Mannitol.