When I install a fresh copy of Windows 98 I usually update it using Windows Update Restored. After that, these are the few utilities I install after:

• 7-zip v9.20 - Free compresison utility.
• Midtown Madness! - Fun racing game!
• Visual Studio 6.0 MSDN Disc 1 MSDN Disc 2 - Coding IDE thingy. Fun to mess around with and whatnot. You'll need all 3 iso to install, start with Microsoft_Visual_Studio_6.0.iso then it will ask you for MSDN. Key is: 873-0188911
• KernelEx unicows - You will need this for installing newer programs intended for Windows 2000 or XP. KernelEx also requires unicows.dll so before installing KernelEx run unicows.exe and set directory to C:\Windows\System.
• Window Installer 2.0 -You probably dont need this, but this is needed for some later/newer programs
• FileZilla FTP Client v2.2.15 - Good for transferring files from another computer. It's getting a little harder to find Win98 versions. Not sure if this is the last version that will work it, but it's been working good for me with no issues.
• Internet Explorer 6.0 with Service Pack 1 - Last version of IE for Windows 98SE.
• .NET Framework v2.0 - You may not need this, but a few programs I've downloaded here and there wanted this.
• NUSB v3.3e - USB drivers for thumbsticks, etc.
• Process Explorer - A Task Manager-like utility. I personally just copy it to my windows directory as taskmgr.exe so I can do a ctrl+r->taskmgr.exe and force close a program. I even add it to my startup folder and you can just minimize it to the tray. Closing programs with this utility is a lot more reliable than CTRL+ALT+DEL and plus it shows everything running.
• Plus! 98 - A optional addition to Windows 98. Adds an Anti-Virus, themes, built in .zip compatiblity, and other features. Key is: 468-4249261
• BTW this is mostly skidded from Windows 98SE Utilites, just with a couple more things that I added so check out that website too.