The problem arises because you are using 16-bit Windows 3.1 applications which cannot take advantage of pre-emptive multitasking in Windows 95. Pre-emptive multitasking allows programs to interrupt each other easily while processing. Some Windows 3.1 programs use cooperative multitasking, which limits a program's ability to interrupt another to certain points in its execution. Even with several programs open, in most cases only one program is doing any processing, and Windows 3.1 easily switches between idle programs. But if you have several programs running at once, ie receiving a fax while you are word processing, everything slows down.
Various things might be done to reduce the problem. Some screen savers use the processor more than others. The scrolling marquee hardly uses it at all, while the 3D screen savers that come with Windows 95 OEM Release 2 -- though spectacular -- are very processor-intensive. Changing screen savers should benefit both Windows 3.1 and Window 95 applications.

For DOS programs, you can disable the screen saver altogether

For DOS programs, you can disable the screen saver altogether. If you right-click the program's icon and choose Properties you will see a dialogue box that will allow you to configure the screen saver option. Click on the Misc tab and uncheck the Allow screen saver box. Whether the program is maximised or running in a window, the screen saver will not interrupt execution.
Windows NT runs Windows 3.1 applications differently from Windows 95. NT converts Windows 3.1 API calls to native 32-bit API instructions. Though they run slower, Windows 3.1 programs can take advantage of pre-emptive multitasking when run on NT.
Last but not least, Windows 95's support of 16-bit applications was meant to make the transition from Windows 3.1 easier. It was not meant as a permanent solution. Upgrading to Windows 95 applications should be the long-term strategy.
- Roy Chambers