I have suggestions/comments:
Commodity Module:
As far as "how do you load them in if there are other modules next to it", I'd say that the restraining clamps/arms open up either swing open on the "L" joint, or the whole arm and terminal chunnel somewhat fold back into the main jetty, though there'd have to be a space in the side of the main arm for that to happen, so the former is more likely/more physically tangible (being clamped in rather than slid in). That being said, looking at the pictures available, the commodity shops themselves would have to be loaded from proximal to distal via ground guide and small tug operations, because direct ship docking at that close proximity to the depot, or to neighboring modules, might be accident prone. To respond to "What if you had the distal commodity shop only, but then recieved the proximal shop?" Well, I doubt inconvienence has be cured in the future, and the station manager would be hopping mad over the complications it would cause.
Would I change anything?
Just add a little swing motor/ditty to the corner of the "L" arms, perhaps reinforce it with something due to its new functionality, and that technicality in my eye is solved. Everything else is great.
Refinery Module:
I see this and I think something is missing. I know it's the future, but it's not that kind of future yet, which means total efficency has not yet been achieved. There's no steam/smoke/heat being vented. I mean sure, one pod could possibly be a milk processing plant, but I'd doubt that there is a universal milk producer/distributor that needs space depots to aid the process. More than likely, refineries in space are working with higly volitale, toxic, and/or combustible materials that would place a habital planet at great risk if it was located on a planet's surface. Also, though the lack of it might be for the sake of design/detail/ploycount simplification, but there are no catwalks or service points where spacewalkers could get out and correct pump/refining malfunctions. But that's a minor nickpick. Finally, since most refineries deal with liquid substances, wouldn't it make sense is there was a "fueling point" at the end of the module for tanker ships to hook up and load up? Although, there is a answer to this in a module you made that I'll get to later on.
Would I change anything?
Not sure how the engine would deal with it, but maybe a smoke tower or two venting something might add the little garnish to the overall feel for the refinery module. Possibly have a small but noticable central operations spire/deck that would serve as the main pump control room for the refinery. Finally, if the comment I'll make later on isn't feesable, add some kind of "fueling point" for stop-and-go transport tankers.
Hydroponics Module:
Perfect.
Would I change anything?
No.
Fuel Module:
Wow. The design makes a lot of sense. Now, going back to a question/suggestion I posed back in the refinery module, "wouldn't it make sense is there was a 'fueling point' at the end of the module for tanker ships to hook up and load up?" Those things could answer that gripe: direct storage of refinery processed materials. However, they are far closer together than nextdoor refinery modules, and might make multiple diligent transfers unsafe. So, why not alter the attachment point to have the ability to flex up and out, spreading the individual tanks out should they need to for loading and unloading purposes? Solves the issue with large scale distribution of refined materials for large transports too big to dock in the hanger.
Would I change anything?
Just add the flexing mechanism.
Now, not to make more work for you, but a few possible ideas for you to add to the depot.
Entertainment Module:
There was a comment thrown in about an obnoxious sign being placed somewhere for the hydroponic module, but it would be better suited for this kind of module. Rather than a theme park in a space bubble, I would see the EM more as a highway truck stop rest station, much like a Flying J or TA. Something more than just a bar. Contained within would be a place to eat slightly more classy than an automat, an understated casino/game room, a one screen movie theatre, warehouse style mini-mall/thrift shop, something along those lines. For the depot, it's not overdone like Privateer's Pleasure planets, more like a good stopping point for an independant trucker looking for a good excuse to get out and stretch, telling himself, "Right, the next Dairy Queen sign I see, I'm getting off and getting me a Blizzard." I'd probbably say things like these, for simplicity and for slight campiness, are one franchise.
Combinations of Modules Produce...
Looking at the pictures provided, especially the one of the hydroponic/refinery/commodity depot, had me thinking what could that depot be producing. My imediate answer was "pharmacuticals". So therefore I think, other than the module's specific production queue, the sum of the collected modules produces a specific commodity that you'd typically find planet side. Another example would be all commodity modules. The shop would have a lot to sell, though probbably not anything perishable as it's more like a warehouse, and would "produce" large machinery and prefab equipment. Stuff like that.
Can't think of anything else, I'm liking what I see here so far.