For what it's worth, here is what I use during a (US English) Windows 98 SE build:
Microsoft Windows IE 6 SP1 Update (No Media Player) (No single installer for this)
Microsoft Installer Version 2.0.2600.2 (InstMsiA.exe)
Microsoft Media Player 6.4 (mpie4ful.exe) and Codec package (wmp6cdcs.exe)
Generic USB 2.0 Mass Storage Driver (nusb33e.exe)
CRITICAL UPDATES
Telnet Update: Security Update, September 9, 1999 147 KB
TelnetUp.EXE
811630: Critical Update (Windows 98) 499 KB
811630USA8.EXE
238453: Security Update 1, November 29 1999 197 KB
238453US8.EXE
256015: Security Update, March 17, 2000 222 KB
256015USA8.EXE
Q313829: Security Update, March 7, 2002 834 KB
q313829.exe
245729: Security Update, November 12, 1999 169 KB
245729US8.exe
259728: Security Update, May 19 2000 193 KB
259728USA8.EXE
Q323255: Security Update (Windows 98) 496 KB
323255USA8.EXE
Q323172: Security Update (Windows 98) 214 KB
323172USA8.EXE
273991: Windows Share Level Password Update 210 KB
273991USA8.EXE
Q329115: Security Update (Windows 98) 407 KB
329115USA8.EXE
Q329414: Security Update (MDAC 2.1) 814 KB
q329414_mdacall_x86.exe
814078: Security Update (Microsoft Jscript version 5.6, Windows 98, Windows Millenium Edition, Windows NT 4.0) 361 KB
js56men.exe
816093: IE Security Update Microsoft Virtual Machine 5.1 MB
msjavwu.exe
823559: Security Update for Microsoft Windows 305 KB
823559USA8.EXE
819696: Security Update DirectX 790 KB (IF DX8 installed)
DirectX8-KB819696-x86-ENU.exe (DirectX 😎
DirectX9-KB819696-x86-ENU.exe (DirectX 9)
330994: April 2003, Security Update for Outlook Express 6 SP1 1.9 MB
q330994.exe
890923: April 12, 2005, Cumulative Security Update for Internet Explorer (890923) 3.54 MB
IE6.0sp1-KB890923-Windows-98-ME-x86-ENU.exe
888113: Vulnerability in Hyperlink Object Library Could Allow Remote Code Execution 176 KB
888113USA8.EXE
891711: Vulnerability in Cursor and Icon Format Handling Could Allow Remote Code Execution 149 KB
Windows98-KB891711-v2-ENU.EXE
891781: Vulnerability in the DHTML Editing Component ActiveX Control Could Allow Remote Code Execution 151 KB
IE-KB891781-Windows-98-ME-x86-ENU.exe
896358: Vulnerability in HTML Help Could Allow Remote Code Execution 496 KB
Windows98-KB896358-ENU.EXE
Q329414 Security Update (MDAC 2.5) 814 KB
q329414_mdacall_x86.exe
308567 Security Update November 20, 2001 (Windows Media Player) 789 KB
wm308567.exe
Q320920 Security Update Windows Media Player 6.4 935 KB
wm320920_64.exe
KB870669 Critical Update for ADODB.stream 104 KB
Windows-KB870669-x86-ENU.exe
KB873374 Microsoft GDI+ Detection Tool 214 KB (Requires MSI Installer)
gdidettool.exe
KB833989 Security Update for Internet Explorer 6 Service Pack 1 1.0 MB
IE6.0sp1-KB833989-x86-ENU.exe
KB837009 Cumulative Security Update for Outlook Express 6 Service Pack 1 1.9 MB
IE6.0sp1-KB837009-x86-ENU.exe
KB904706 Security Update for DirectX 8 or 9
WindowsME.Windows98SE-KB904706-DX8-x86-ENU.exe
KB908519 Security Update for Windows 98
Windows98-KB908519-ENU.EXE
KB916281 Cumulative Security Update for Internet Explorer 6 Service Pack 1
IE6.0sp1-KB916281-Windows-98-ME-x86-ENU.exe
KB917344 Security Update for Windows 98
Windows9X-KB917344-x86-enu.Exe
KB918439 Security Update for Internet Explorer 6 Service Pack 1
IE6.0sp1-KB918439-Windows-98-ME-x86-ENU.exe
KB918547 Security Update for Windows 98
Windows98-KB918547-ENU.exe
KB913433 Security Update for Flash Player
Windows-KB913433-x86-ENU.exe
RECOMMENDED UPDATES (Any order after Critical Updates)
273017: Windows IDE Hard Drive Cache Package 224 KB
273017USA8.EXE
Root Certificates Update 189 KB
rootsupd.exe
Agent 2.0 391 KB
msagent.exe
260067 Mapped Drives Shutdown Supplement
260067USA8.EXE
Note that if you use a different version of IE or Media Player, you will have to use different updates than those given above in certain cases.