Here are few utilities I install after a fresh 98SE installation:

• 7-zip v9.20 - Free compresison utility.
• 98SE2ME - Nice utility to copy over the better parts of ME and get some updated TCP stacks and other performance and stability. I've used this on some older machines like a P1 166 with no ill-effects.
• DirectX v9.0 - You will need this for some later 3D titles.
• 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.
• KernelEX v4.0 - Emulator to allow some newer software designed for Win2k and XP to run on Win98SE.
• .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.
• Opera v10.61 with MSIMG32 DLL - The MSIMG32 is to help with some rendering effects. A trick I use is to force the Opera Turbo on and it will do a lot of prerendering for you offsite. Good for slower computers (like p2 and below).
• 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.
• Unofficial Windows 98SE Service Pack 2.1a - Includes all hotfixes and security updates for Windows 98SE.
• TightVNC v1.3.10 - Last version of TightVNC with Win98SE support.
• TweakUI for Windows 98 - Customize your Win98SE.
• Windows Media Player v9 - Go here for some unofficial updates, including WMP10!