few things to try first
download and run
http://www.ccleaner.com/download
(it may or may not make a big difference ... but it's something everyone should do from time to time)
check the scheduling of any virus/adware scanners - the "sometimes" makes me wonder if it's kicking in at boot time if it's missed a scan (mine does it "sometimes" a pain ... but I generally let it)
the power settings are worth checking
also ... if it's a laptop .... is bluetooth on - network timeouts can take ages to error out ...
I don't see that startup progs in general would slow things down "sometimes" but if you must follow this advice.....
rather than msconfig use
http://www.mlin.net/StartupCPL.shtml - which is easier to reverse (use safe mode).
finally disabling startup options is quite a skillful art ... in XP it was possible to poke and hope ... but vista is much less forgiving
if you don't know what it is ... or what it does ... don't disable it (without research).