I dunno man, I run SSDs and HDDs and I've never seen any slowdowns.
Is your disk really full or something? How much ram are you running?
Maby it is that more apps are starting up when you log on, rather than the default number from a fresh install (which would be like only a few).
I have 10 applications, and numerous other things, such as littlesnitch, Viscosity VPN, iStat, and many many other small addons that start when I turn the computer on.
If you are having a problem you can reinstall OSX over your current drive, there's an option to replace system files and stuff if any got modified. I've had to do that a few times myself.
Apple makes Onyx (google it) that repairs your disk drive.. Maby you can give that a spin.