have you defragmented your drive recently? Defragmenting can help. Also there is a program called BootVis which can optimize the placement of your boot files on the disk to improve boot speed. This is a program by microsoft, however it is no longer supported (try google to find it), and while it works (I use it on my computer), you take a risk in using unsupported software... so keep that in mind.
Also I would check if you have unecessary start up programs. Go to Start-->Run and type "msconfig" (without quotes)
Go to the Startup tab and uncheck all unecessary startup items. If you are unsure of whether a program is necessary or not you can either google it or check here:
http://www.sysinfo.org/startuplist.php
Finally, although your drive is 90% full, this does not need to adversely affect performance. One of the best solutions to this is to split your drive into two partitions... one containing windows system files and application data, and the other containing misc files such as documents, music, backup, storage, etc. This will also significantly decrease drive defragging times.
And, of course, scan for viruses and spyware. I recommend the programs
hitman pro (anti-spyware) and
avast! antivirus. Both are free. Also, just to round out the holy trinity, a great free firewall (better than some commercial ones) is the
Comodo Firewall.
Hope that helps. There are a lot of reasons why you could be seeing slow boot, program load times... but defragmenting, removing unecessary startup items, intelligent partitioning, and clearing any and all spyware/viruses should definitely help.