How to speed up my system- reboot from time machine or increase free space?

I've just upgraded my system to 3GB ram and some actions are being quite sluggish still- this I would suspect is because I have only 3GB free on my 120GB hard drive.
Would rebooting the system from a time machine backup speed up the computer- in that all the files should be continuous or should I just aim to make more space on the hard drive?

Ouch! You need to delete files - it's not a fragmentation issue, but a lack of available space for virtual memory and swap files. You should always have 10-15% of your capacity free (so, for you, that means keeping 11-16 GB free space on your drive).
At this point, I'd recommend deleting files to free up space, then running Disk Utility > Verify Disk (and if errors are found, boot from the Install DVD and Repair Disk).
To find your largest files, use something like Disk Inventory X:
http://www.derlien.com

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