Since the Apple IIgs doesn't have coprocessors to manage disk access and the serial ports, either of these requires the complete attention of the main 65816 processor. This can wreak havoc in an environment with slow disks or high-speed serial links, as accessing disks usually results in turning off interrupts for the duration of the access. This situation is lessened considerably with a DMA disk controller, such as the Apple High Speed SCSI or CV Technologies RamFAST. But this isn't as bad as it sounds; the IBM PC and Apple Macintosh also suffer from this problem, and the solution is robust programming. Make sure your communications protocol can handle errors where expected data doesn't arrive quite on time, or in full. The best solution would be an add-on card with serial ports and an on-board processor to make sure all serial data was received whether or not the main processor was busy (this is a hint to some enterprising hardware hacker, by the way).
Yet another concern for GNO/ME applications is file sharing. GS/OS provides support for file sharing, but it is up to the application author to use it via the requestAccess field in the OpenGS call. GS/OS only allows file sharing if all current references to a file (other instances of the file being opened) are read-only. GNO/ME authors should use read-only access as much as possible. For example, an editor doesn't need write permission when it's initially reading in a file. Note that the fopen(3) library routine in ORCA/C 1.2 does NOT support read-only mode (even if you open the file with a 'r' specificier), but it does in ORCA/C 1.3 and later.