I've got a Topeak MTX Trunk Bag DXP. Used to have some Bontrager Panniers, but those were actually too big and messed with my aerodynamics (40 miles round trip, windy season... it made a difference.)
The trunk bag has one large compartment, and 2 side pockets that unfold to expose panniers. 99% of the time I can fit everything I need into the main compartment and leave the panniers packed up. So here's my typical load. The large compartment is split into 2 halves using an adjustable velcro divider.
Left half (standard kit, stays packed no matter if I'm commuting or funning):
* 2 tubes, multi tool, tire levers, 2 CO2 cartridges, CO2 inflator, Adjustable wrench, 8 SRAM power links, 10 links of extra chain, scraeder-to-presta valve adapter, patch kit, tire boots; all in one gallon ziplock bag.
* Folded up paper towels, in another ziplock bag
* Band aids, neosporin, bandages, in another ziplock bag. Will be replacing this with a hardshell kit that takes up less space soon.
Right half:
* Cable lock coiled up.
* Rubbermaid 24oz plastic container holding my lunch.
Then on top of those I can fit my U-lock, and place my keys on top. So when I get my bike ready for the commute the night before, I simply pack the cable lock and the lunch (if it's non-perishable), put the U-lock on top, and drop my keys in, and zip it up.
In the side pocket I have a separate ziplock bag with my wallet, phone, and keycard for work (so I can just bump the bag up to the key reader and it will let me into the office).
If I have commuted to work too many times in a week and ran out of backup clothes at work, then I must transfer some clothes as well, in which case I break out the right pannier and stuff the clothes in it.
On days like today when I am going to hit up the grocery store after work, I fold up my Topeak Chopper HB basket, and it fits entirely within the right pannier. Then after work I go shopping, remove the basket from the pannier and mount it on the handlebar, then load up the basket and panniers with the groceries, and ride home.
Additionally, since the weather has gotten a little strange and temperatures can vary greatly between daylight and moonlight hours, I decided to bring my backup long-fingered gloves, balaclava, and 2 lights (since it'll be dark after work now). So these went into the left pannier. Hopefully this won't affect how many groceries I can fit on the bike tonight. We shall see.
I'm really loving the trunk bag. It's slightly more annoying to access my spare tubes and tools because they're packed pretty tightly, but given the frequency of that is relatively rare, I find the aero benefits of being able to fold up the panniers are worth it compared to the slight inconvenience of things being packed a lot tighter. My average speed went from 12mph to 14mph on my route. Over 40 miles that makes a big difference.