I use different ore processing systems for different ores, that way I get to use lots of different mods and my base doesn't look empty.
For silver, dark iron, cobalt and ardite I use Factorization (including crystallisers). This was the most ambitious cross-mod build I did and it was very satisfying in the end.
For gold, iron, copper, tin, nickel and lead I use Engineer's Toolbox. It is a really good mod and the kiln makes a nice centrepiece in my main ore room. On some ores the effective output is *4 which is good enough for me.
Yellorite goes into a Sag Mill because of bonus cyanite.
I was going to use Mekanism for all my ore processing but I ended up limiting it to osmium only. I did get to the *5 yield stage but producing enough of those reagents was difficult. I made 2 max sized salination plants and I barely had enough brine to process the ores (very very power guzzlingly slowly) let alone turn my gunpowder into sulfur. It was fun and engaging, but I only had enough patience to stabilise the production of reagents when I only had to process my osmium. How does my experience square with all of you Mek fans? Does it sound like I am screwing up?
Bauxite and rutile go through mariculture like I mentioned earlier and I am working on getting those fancy upgrades. It requires some mariculture progression (fair enough) so I'm working on that. Got a nice automated pearl shop earlier. Making that was harded than I anticipated, but it was fun. The purity upgrades need a lot of white pearls.
Every remaining ore goes into a rock crusher from railcraft (with the help of an addon mod*) and all the random dusts and crystals get smelted in an upgraded mek factory.
My favourites are Factorization and Engineer's Toolbox. They don't have the highest yield of all the systems available but Factorization is so aesthetically pleasing to me and both mods have a large design space and encourage me to be creative. I also happen to be good at them so that helps
*Not sure what this mod is called but it adds loads of recipes to the rock crusher (and maybe some other machines) and it is at least in Resonant Rise.