I'm planning to use an SSD as my boot drive and my HDD as the storage drive. Does it matter how much storage is on the boot drive? Would a 64GB SSD be different to a 120GB SSD?
Specifically:
Samsung 840 Series 120GB vs Sandisk Ultra Plus 64GB
It depends on you and your needs. I for example have a 60 gb SSD which I use for my operating system and programs and I have 36.5 GB free on it with all the programs I can use installed. I can't imagine someone filling all the free space with programs since most of them occupy anywhere between 5-60 mb of space and the OS is pretty light (Windows 8).
After a year or so, Windows will have filled up about 60 GB of uselessness, so definitely get the largest SSD possible. An SSD only perform max when it's not more than 75% full.
I'll also recommend buying the bigger SSD. Take a look at the new iteration of Samsungs 840 series, the EVO. They are cheaper (as in Price per GB) and faster than the SanDisk you posted.
Ask yourself these questions: How often do you restart your computer? How often are you starting a program?
And then go buy the bigger SSD and put all your programs on it (or at the very least the ones your use most frequently).
On a sidenote: I am using a 512GB SSD (Plextor M5P) as my bootdrive and use 379 GB of the available space. This is because I have my Steam folder on the SSD, which in itself uses ~290 GB. It really depends on what you want to do with it.