The latest Axe-Fx firmware update really made a huge difference for me. The compressor is awesome now and the highs on all the models are much more pure sounding. I've got an interesting little rig going on now. I run my bass into the Ultra and have my laptop interface strung through its effects loop. That's really opened up a lot of options for me.
For one, there just really isn't anything even close to the Axe for tube amp simulations at all. It took me a good while to get comfortable with tweaking the amps for bass but there really are several simulations that I don't think I could live without now.
I've made variations on the "Tube Pre," "Jazz" (Roland JC-120 Jazz Chorus), "59 Bassguy" (Fender Bassman), "Double Verb" (Fender Twin Reverb), "USA Clean" (Mesa Boogie MkIV Clean), "Buttery" (Budda Twinmaster), "Jr. Blues" (Fender Blues Jr.), and "SV Bass" (Ampeg SVT) models. I've definitely found the Fender models to break up in a really smooth way when set right for bass. The Tube Pre is straightforward but beautiful. As I've gotten better at editing patches, I've really warmed up to the SVT model in a big way.
I had been kind of down on the 8x10 cabinet model for a while and usually stuck with the 4x10 as my main cab, occasionally adding an auxiliary 1x15 or 2x12. But lately I've been really digging the AKG D112 model on the 8x10. I'm going to experiment with impulse response cabinets and see if GreenBoy might be willing to help design an IR for one of his 15/6/1 cabinets. I'm using one right now and it's been perfect with the Ultra.
The 5-band parametric EQ's are great and as of the last firmware update, the compressor block is actually very good and provides zero-latency compression with minimal artifacts when I need it. Overall, I find the Ultra very flexible as an amp but am constantly amazed at how natural it sounds.
A lot of the stuff I'm working on now calls for a less natural and more processed sound. So actually, I usually run my input signal straight into a subtle compressor and then split it two ways with one half of the signal going to a tube amp on the Axe and the other half going to my laptop via the Ultra's routable FX loop.
In software land, I'll aggressively scoop my mids and then proceed to shape the low and high end exactly as I'll need it for the track. I use Fabfilter's Pro-Q to carve the mids away. Then, I'll use a fancy "color" EQ or saturator to add harmonics and density to the lows that aren't so much heard as they're felt psycho-acoustically. The Nomad Factory Pulse-Teq EQ is great for this sort of thing because you can boost the lows until you get the right kind of saturation going on, and then attenuate them with a second knob without losing the coloration. I basically do the same thing to the highs until they get crisp but not annoyingly so.
I'm usually over-driving the Pulse-Teq as an effect so I tend to low-pass everything to remove any harsh highs and then smooth it all out with a limiter of some sort. I'm also really digging the Stillwell Vibe-EQ for stuff like this. It has a great sound and it's $39.
Meanwhile, I carve the lows and highs out of the tube amp signal on the Ultra and isolate the parts of the sound that are most audible in the mix, roughly 400hz-2khz. I mix the two sounds together with a Mixer block and then maybe run them through a really light compressor if they need to be glued together anymore. Sometimes I send both of them to a cab sim, sometimes just the Axe, sometimes each signal gets a different cab, it depends on what I'm going for.
Synth-wise, things have gotten CRAZY every since I decided that I wanted to preprogram automation for stutter effects, granular pitch shifters, distortions, reverse delays, etc. on stage in Logic 9 but so far so good. The basic formula is Bass->Synth Block(s)->Compressor->Hard Noise-Gate Side-chained to dry input signal->lots and lots of stuff. I can definitely cop some gated fuzz tones with combinations of the Ultra's Drive and Amp blocks.
I'm also using Ohm Force's Ohmicide as a multi-band distortion and dynamics processor/gate. Nothing every leaves Ohmicide with a sloppy envelope period, and I have a lot of control over the frequency balance in a way that sounds much more extreme and angular than EQing would. Check this plugin out it's amazing.
I've got a few software filters that I really dig. Ohm Force Quad Frohmage is without a doubt the deepest and nastiest of the bunch with a ton of filter models including a great "Moog" filter, saturation and overdrive options, 4 filters in serial or parallel, very nice envelope follower, etc. The filter in U-he's Uhbik is also top notch and very easy to use.
For anything that needs more phatness, I bust out Camel Audio CamelPhat. It's a fantastic coloration tool with a filter, envelope follower, tube overdrive, distortion, bitcrusher, exciter, EQ, hilariously exaggerated compressor, band-pass filter, LFO, flanger, it's a ton of fun, sounds great, and doesn't take much of a hit on my CPU.
Fabfilter Volcano 2 is definitely the most powerful filter I've come across and it has a TON of modulation options, filter models, side-chain options, etc. I use Volcano for beat-synced LFO filtering, stepping wobble basses, anything flashy and fun that would have either been intensely time consuming or borderline impossible with hardware. I'd like to try out the SoundToys FilterFreak at some point but it's a) very expensive and b) I already have a ton of filters.
This post is already way too long but if anyone is interested in using a MIDI-foot controller to trigger sequenced effects with crazy MIDI routing in your DAW, give me a holler.