I have a 6990, directx 11 capable card, but black mesa is only running at max directx 9 and the boxes to select otherwards are greyed out. I know directx 11 is working from several other games. Is this max for black mesa at the moment? or is there a problem here?
That’s just this version of the Source engine. Choosing to use DX11 wouldn’t do any good anyway, unless the engine was written to make use of it.
I have some different stuff over here. At Working PC (8800GTX, 295.73) I can select AntiAliasing up to 16xQ CSAA, but at my regular PC (GTX560ti, 306.23) I can select only up to 8x MSAA. Have to try with HL2 but it is not a mod issue I belive (it is not an issue at all to be honest) 
Source does not support DirectX11. It doesn’t support DirectX10. It supports DirectX9 and DirectX8
Was 16xS available in BMS or in some other Source-based game? BMS uses Source SDK 2007 version which is slightly outdated compared to what Valve had used for HL2:EP2. Thanks to that BMS can’t use mat_queue_mode other than 0 (i.e. the engine hangs when trying to offload mat-related stuff to a separate thread) and have some other limitations like one we had in HL:EP1 and Portal. For example on my home PC I could select 16xS AA in EP2 but can’t do it in Portal or HL2:EP1.
TBH you’d better set AA to be 2x or 4x in BMS and then create a profile for BMS in nVIDIA CP (actually, modify existing HL2 profile - BMS and HL2 share them) and set there AA to “Enhance application setting” and select the AA level you’d like to use. If you’re an advanced user - download and install nVIDIA Inspector and use it to manipulate HL2 profile. You could force the game to use SGSSAA in that case which is one of the best possible AA methods wrt rendering quality. Be warned that the performance is likely to be pretty shitty on your 560 Ti if you’d use anything higher than 4xSGSSAA.