Here are a few of my most-frequently-used utilities; the things I prefer to have available whenever I set up a new Windows system. All the downloads here are in ZIP files, because I can't ftp self-extracting EXE files. Mostly these work with Windows 95 and 98 (most flavors, but I WILL NEVER use ME, and have no great desire to get into the world of XP and .NET), NT 4, and 2000 Pro. That alone tells you that they aren't truly heavy-duty, of course. But they help me iron out a few of the little bumps in the road, and avoid having to invent new work-arounds all the time.
I haven't tested these things systematically. I just put them on most of the systems I touch, for my own convenience in supporting them. Many times, I don't even tell the user they're there. But when I go back to maintain a system, I like to see these. These are mostly things that have been around for a few years, and are all (AFAIK) freeware. I didn't go to any great trouble to look for the absolute latest versions, because these are the versions I'm using right now.
AtomTime95 (73KB) is a decent little internet clock synchronization utility that checks your system clock against the atomic clock in Boulder, CO, or another clock that you may specify. No bells and whistles; this the older freeware version.
AVG Antivirus System (5 MB) is free for personal use. You supply a valid email address, they email you a serial number. You'll need it for the actual installation.
DOS Here (1 KB) is a little INF file that came with one of the old PowerToys from Microsoft. It just adds another item to the Windows right-click popup menu, opening a command prompt window and logging into whichever folder you right-clicked on.
FTP Explorer (662 KB) is a decent little ftp utility, that looks and acts pretty much like the Windows Explorer. You can drag and drop files between local drives and ftp sites, as if the ftp sites were just more local folders. I used this on the not-infrequent occasions that Front Page 2000 choked instead of publishing. Now I use Macromedia Dreamweaver, which has a built-in facility that is almost identical to FTPX.
NotePad Plus (198 KB) is (duh) a Notepad replacement. It works by simply replacing notepad.exe with an identically-named but much more capable file. Yeah, I know, QAZ trojan yadda yadda yadda... I was using this one long before the worm debuted, and it still works for me.
Popup Killer (2.6 MB) automatically closes popup windows in your internet browser, like those annoying X10 camera ads that glaringly imply that you should use them to spy on pretty girls. You can add new popups to the list, as well. HIGHLY Recommended. (The Opera 6 browser includes the ability to turn off all popup windows. Nice.)
RegClean (335 KB) is fairly well-known as a pseudo-Microsoft (unsupported) registry-cleaning utility. As Dave Farquhar observed in his excellent book, Optimizing Windows for Games, Graphics & Multimedia, it doesn't compact the registry database, but it does remove many invalid references. Fixes some minor problems, and I've never yet had to use the Undo files it creates. For yucks, run it sometime immediately after installing only Windows and Office. It surprised me a little the first time I did it, but only a little. ***DO NOT RUN IT UNDER WINDOWS 2000.*** Thus quoth Microsoft.
Startup Manager (567 KB) has long been one of my favorites. Almost everything that software vendors insist on starting at boot time is useless garbage. And the rest is highly questionable. Actually, I've been using this since Windows 95 days, but a similar capability is built into Windows 98 (possibly starting with Second Edition?), called MSCONFIG.
TweakUI (83 KB) is an update of the TweakUI that first came with Microsoft's PowerToys for Windows 95. This one has only the TweakUI portion, not any of the other toys, but I like to use it to do things like remove unwanted icons from my desktop in a toggle-able (is that a word?) manner, speed up menu display, and so on. This version works with Windows 95 through 2000.