Aligned programs are stored in 4KB blocks of data on the HD
Windows handles internal memory in specific chunk sizes (4KB) called Pages. Non-aligned applications are not stored (on the Hard Disk) in these chunk sizes and therein lies a problem. The non-aligned have to be->made to fit' into memory's 4KB Pages.
MapCache is the in-built Win98 program that moves applications in and out of memory areas. In the case of non-aligned programs it has to fit (to map) the code from your Hard Drive into the memory Page structure that Windows requires - so that each segment starts on a 4K boundary. The->mapping' takes some noticeable time in the case of large applications.
Obviously, if your larger programs on the Hard Disk are already pre-aligned, they would load faster and use less memory. And they ARE faster.
Most of the code in Win98 is already aligned (the core OS components and applets, for instance). However, all the CD's third-party applications are probably unaligned and the larger ones should benefit from being aligned.
Only the executable files (.exe and .dll) must be aligned and care must be taken not to align certain types (more later). Over the next few years most new applications can be expected to come pre-aligned. However, until then, there are plenty of large applications out there that will benefit substantially. Aligning small programs is simply not worthwhile and increases the risk of encountering a problem.