Fujitsu Siemens has used standard ATX cases for their SCALEO tower series. The Pentium 3 generation cases are a bit ugly though, the nicer ones are from 2001 and forward.

My parents Pentium 3 generation Scaleo upgraded with a Fujitsu Siemens Socket-754 board and a A64 3200+ from a newer Scaleo was in use until a few weeks ago when I gave them a "new" computer.

I know Gateway 2000 was a big user of AT and ATX cases.

Time Computers (UK)
Tiny Computers (UK)
Atlantic (UK/DE not sure)

Both used standard cases and motherboards. Time were the better of the two, usually employing low-end parts from Seagate, ECS and SiS that were slow but got the job done. Tiny used Chinese junk and it sometimes had reliability problems. As for Atlantic, if anyone ever finds one (Makro sold them) I might want to buy it and at the very least would appreciate a picture of their OEM Logo sticker.

Falcon (Maybe a local builder)
And one which is definitely local, Golding, who used good quality parts (QDI/SuperO/Matrox) but as stated were a local company (From Hull) who didn't distrubute much outside of the city. Still useful info for any "hullites" that might browse here.

Oh, and Akhter (Indian/British to my knowledge) - They used decent components inside Mitac cases usually.
Stone Computers (UK) commonly found in government/educational institutes. Cases were usually from companies like K&M Group.

There were a lot of local shop P2/P3 OEM builds were done with AOpen kits and they are standard ATX. There are other examples of kits like this but I cannot think of one... maybe ASUS... I can't remember.

Gateway 2000 P1/P2/P3 systems are hit and miss. Most of them will not take a standard full-size ATX PSU. The really large cases still come with the smaller Gateway PSU but will take a full-size PSU. I know where an example of a large tower P2 450 is and if I have time I will grab it and take some pics.

Premio used standard ATX as best I can remember but not sure how wide spread they were.

I'll try to think of more later.