Yes, I agree that VD has been crassly commercialised and it's really nauseating for the single folk out there.
But no-one's making you buy the crappy pre-written card, the box of supermarket choccies or the wilted roses. Use some imagination and give something personal.
If your loved one shares your geeky tendencies, then don't say it with roses, say it with geekery. :) Unlock Warrant's Cherry Pie for her on Guitar Hero. Let her kick your arse at Wii Cow Racing. Hunt down her favourite classic game from the discount bin at EB and install it on her computer. Promise you'll sit through "Pirates of Silicon Valley" or "Real Genius" with her (again). Get her an xkcd t-shirt. Buy the 2nd controller for your console game of choice so she can play with you. Stop raiding with your World of Warcraft guild for one night and level up your lowbie Warcraft toons together like you keep promising you will.
Are you planning anything for Valentine's Day? If you have any awesome geeky.gift ideas I'd love to hear them.
Disclaimer: This list is not entirely my own personal wish list. I have no wish to play Cherry Pie on Guitar Hero.