There's nothing wrong with MeGUI. Sharktooths profiles are great.
Anyway. I use a combination of things depending on what I'm working on and what to do.
TMPGenc Xpress 4, offers everything you have asked about. It even have some pretty decent filters and CUDA support for them (so if you have a Nvidia GPU that supports CUDA, you can run your filters on the GPU and decrease encoding time).
However when I am working with really bad sources, or stuff that needs to be deinterlaced in funny ways, etc I will switch over to Avisynth / Vdub.
For finished DVD, Blu-Ray, or DivX Ultra (DVD menus) projects, I'd go to something like TMPGenc Authoring Works 4.
Otherwise I'll jump over to MeGUI and do an x264 2-pass with one of Sharktooths profiles. Then mux it up into an MKV if it needs multiple tracks.
So you have quite a few options. TMPGenc's stuff obviously can be "found" in various places, but its really a fair price for what their tools can do compared to Complicated crap like Vega, Premiere, and other "Pro" tools which I find too complicated and useless for my needs.
After you get your tools, its a matter of reading. Google, Videohelp, Doom9. All you need to learn stuff.
As for the Google trolls, BFD, at least he said he had tried looking and wasn't finding the answers he needed. Beats the hell out of the 99% of people that just don't bother to try in the first place.