I have only played the PC version, but I have seen people play the table top version and I have studied it to see if I would find it interesting. I didn't, the table top version seems rather boring to me and I think the PC version is much better.
I don't think they're really comparable, the gameplay elements don't really match up in any way shape or form. It's like comparing a FPS to an RTS or an MMORPG. Or comparing horror or action movies to character dramas or a comedy film.
i preffer the pc games ( dawn of war2 for example) mainly because there a lot more action packed exciting and you dont need anybody else to play it and it doesn cost£50+ for an army even for just display value i think that properly painted models just look awesome though.
But tabletop is also fun cause you can paint your guys and you kind of build up a realationship with your mini-army. On Tabletop you feel more like they're ' Your ' troops as your the one who bought them, assembled them, glued them, and painted them.
However on the PC version you just buy them with a virtual currency.