Well my theories are riddled with slash, of course. But, lately I've been thinking back to House's previously relationships/flings (minus Lydia because Wilson didn't know about her, as far as I know) so Cameron and Stacy. With Cameron, Wilson warned her not to hurt him, and seemed to lightly encourage House to pursue her and teased him about her a little. With Stacy, he advised against the relationship...and then yelled at House when he threw it all away. With Cuddy, it felt like there was absolutely no conflict, no concern; the moment he found out they'd kissed, he insisted that House date her. Now, when House kissed Cuddy, it was after Wilson had come back after leaving when Amber died. He claimed that he left because of House, seeming overwhelmed by their friendship. I feel like during that time he was gone, he could have realized his feelings for House. When he came back, he was hurt and angry at himself for asking House to put his life in jeopardy for Amber. He just wanted things to go back to normal so he said that he felt that people didn't get to decide who their friends were. After having almost lost House, he didn't want to lose him over possibly destroying their friendship. The slashiness of this might make me think it's just that, ridiculous slash, but the intensity of his insistence makes me feel like he's trying to deter House from how he really feels.

Wilson could have realized his feelings later, but I suppose that's my main theory is that he's hiding how he really feels. Instead of talking out House's concerns, sarcastically commenting as they both examine things, he's done nothing but root for their relationship. Every reason, every concern House brings up, is swept away immediately but Wilson's reassurance. It feels...weird. It feels like he's hiding something. (Of course, this could just be the writer's wanting to make Wilson into a Huddy cheerleader.)

Wilson might not just be concerned about caring for House, but might possibly be homosexual and wanting to hide that. I mean, three failed marriages where he was spending all of his time with his male best friend. Wilson wants to appear societally acceptable, scratch that, it's as though he needs to. Good job and a wife seem to be part of his "societally acceptable" formula. (This also goes into his need to appear caring and polite around everyone, only showing his darker, more sarcastic side and even his flaws in general around House.) If House and Cuddy break up, Wilson might gravitate toward him again and he might fear either slipping and revealing his feelings to House, or coming out as a homosexual. (Or even if Wilson isn't a repressed homosexual, House might be the first man he's ever loved, and he's afraid that he is homosexual)

Anyway, just some theories. I have no idea of their merit lol.