Win9x:
I'd rather have Office 2000 or 97 on a 9x system, just because its UI matches the system's one instead of the WinXP-ish eye candy in Office XP. But they all should work just fine.
Also I stay away from IE6, and stick to 5.5, because IE6 causes some weird bugs in the shell (me being unable to show text on Explorer's toolbars, some hiccups and lags, etc.) besides having XP-like icons and toolbar images.
Firefox 2.x + Noscript works.... but even on my faster K6-2 it feels sluggish. But hey, if you need to browse something quickly it will do a better job rendering modern pages than IE5.5. Oh, and do yourself a favour and disable scrips in IE too. Specially on a slower processor. Oh, and you need some tweaking to revert the menus to the classic style.
Novell Netdrive is great! It allows you to mount FTP folders as drives, and it works much better than using either Filezilla or IE's buit in FTP client.
DOS:
4DOS. Just 4DOS. DOS without 4DOS isn't nearly as fun! Just configure it to go back to uppercase file names, ignore descriptions, and add some colors to the dir listing and you're good to go!
MPXPlay - best MP3/AAC/OGG player for DOS IMHO
DOSSHELL - Whenever you need the task switcher (not very often)
Norton Disk Doctor - I like it better than Scandisk
UIDE (now XHDD/XDVD) - for late DOS systems. Disk caching + UDMA support for DOS
VIDE-CDD.SYS - The CD driver that gave me the least trouble ever
CuteMouse - 1.9.x version is trouble-free on all my systems. 2,0 and 2.1 have issues with some of my systems.