I dont know how to explain this or not even where to point out anything, but i'm just having a fair ammount of performace issues with ubuntu, things like when i click the bar at the bottom the program doesnt come up the first few times, and when it comes up is a bit slow as well, also games trough wine are a fair bit slower, I would get about 200fps on CS:S in windows and only 25 on linux, i understand that there might be a bit of performace loss but that's a tad too much.
My specs are

Intel core 2 quad Q8200
MSI P43 Neo-f
2GB Ram
ATI 4870 1GB

I really am pointing towards the motherboard as i've heard that MSI are pretty crap with linux, any help would be appreciated

Not that it matters, but are your sources really credible as far as the "MSI are crap with Linux" statement? I'm on my second MSI board with Linux, and have had nothing but good things from MSI. They're my #1 board choice. Regardless of who makes a board, Linux related problems may arise from one or more particular devices ON the board, such as a network device, or video card, but claiming a particular mfgr makes Linux-unfriendly boards is sketchy.

Anyhow, it seems you have a decent CPU, adequate RAM and video memory, but I would be looking at your video card first, for the causes of the performance issue you are suffering. Specifically, what video driver are you using? If the performance issues are mainly related to games and/or graphics intensive processes, I'd start there.

ATI combined support+performance is not as good as it is with some other mfgrs video cards. If you're using an open source driver or a driver that doesn't do acceleration or direct rendering, it could certainly cause performance issues.
Depending on what exact "glxinfo" tool is on your system, you might try one of the following:

shell$ glxinfo | grep direct
shell$ glxinfo | grep Direct

and see that it says "Direct rendering: Yes"

Also, you may be able to identify what video driver you are using by one of the following methods:

shell$ sudo lspci -v
shell$ lsmod

Kind regards,
Sasha

well not only in games i use the actual drivers from ATI, games are working a bit better now that i upgraded the drivers, but just performace even just while i'm on the os, opening a new window takes a while, other things like when i open a folder and i wanna go back, i press the back button once then the whole top of the window pretty much freezes and i cant click on it i can only click on the side and start from /, or use backspace, also when i watch movie i just freeze up after like 5 min or so, especially if i'm doing other things at the same time.