I've had these issues for sometime now. Turns out that I may have discovered something crucial about the problems. Rebuilding the datafile, clearing the cache, and removing all InputManagers did not fix the issues, which were reproducible on two Macs. Removing the Internet plugins also did not resolve the issues.
If Safari is starting slow for you under Snow Leopard and you use 1Password 3, make certain that you remove the old InputManager called something like "1Passwd." I was able to start Safari far faster than before. Until Agile fixes the command key sluggishness issue, make sure you lock your keychain after you're done using it. It's a pain in the ass, but your browsing snappiness will return if you like to use key commands like me.
Another discovery (apart from the one listed below) can be read here. Turns out that it's the "key icon" in the Safari menubar that's somehow contributing to the command key slowness in Safari. If I disable that in 1Password's preferences, the sluggishness disappears, even with the keychain unlocked. No clue, but that's somehow the culprit. Maybe it will help others. Please let me know here if you're able to reproduce this problem.
First, I can verify that removing the old InputManager left over from the 1PW 2.x days definitely made Safari (ver. 5) start up faster (2 - 3 icon bounces in the Dock instead of about 10). Start up is almost instantaneous now, thank goodness.
Second, this command-key sluggishness (and even clicking the 1P or key icons) I've been going through has persisted (any Command key combination is slow on Safari 4 and 5). This means sluggish behavior for key combinations like Cmd-T to make a new tab, Cmd-W to close a tab, or even Cmd-Q to quit Safari. Very LONG pauses before the desired result follows the keystroke combination.
However, I made a discovery today that I wanted to pass along to you all at Agile, which may or may not help troubleshoot this issue. It's reproducible on my Mac Pro and my MacBook. The sluggishness ONLY occurs while 1PW is unlocked. As soon as I LOCK 1PW again, the snappiness of my command keys in Safari 5 returns!!! Unlock the keychain, back to sluggishness. Completely reproducible on both my machines.
I have rebuilt the data file and cleared caches several times. The only other InputManagers I still have running are DeliciousSafari and the latest beta of Glims (if that's even still an InputManager).
Any advice you can provide would be greatly appreciated.[From Slow Safari startup with 1Password enabled (when the Cache is out of date)]