Just wanted to share my experience about that 
After several months of research, I've found things that work pretty well :
First, getting a great sound out of the bass and amp is EXTREMELY important.
I had luck to achieve this Meshuggah kind of sound at tracking by doing this :
I splitted the signal outcoming from the bass :
1) First signal going into the amp. Ampeg amps and cabs are killer, they work for me. On the amp, move the EQ to get a great 90-120 Hz sound, thick and warm. Check the 250 Hz area, you don't won't too much of it to keep the clarity. I generally cut some 500 Hz here, but not too much. Then put a mic in front of the amp to capture this, MD421, D112... Route the mic into a good and punchy pre, and then into an EQ. Let's say Mindprint Dual Tube Channel channel 1. High pass at 35 Hz, low pass at 4 khz.
2) Second signal going into a DI for clean sound (something like REDDI, Avalon U5, depends on what you're after... but you need something that keeps your signal clean with thick but balanced bass/low meds and clarity in the 4-5 khz area).
3) Third signal going into a guitar distorsion pedal (POD or Sansamp GT2 for example), then into another DI (let's say API for punchy meds), then into a compressor (1176 works well) and into a parametric EQ (let's say Mindprint DTC channel 2). Play with the gain setting until it sounds good on the strings major hits. Turn down the lows and highs, boost the meds until they fit with the guitars tone if you already recorded them. Too much meds is too agressive, not sitting in the mix and fighting with the guitars a bit. Not enough meds is too dark, the bass sound will end into lacking of definition.
On the compressor, 4:1 or 6:1 ratio should work. -3 or -4 db of gain reduction is OK, with medium attack. Set the release time taking care of the playing : if the bassist isn't very consistant, long release works definitely, if the bassist has a great constant attack on the strings, shorten the release time should be a good thing.
On the EQ, high pass at 300-400 Hz, low pass at 3 Khz. Boost the **** out of 700 or 800 Hz, and 2,5 - 3 Khz, to get something very dirty and raw, than you can hear into the mix.
Listen to the disto and amp sound, they should blend well. The clean DI sound is there to bring back if something lacks at mix time, or to reamp if necessary.
The important thing is to get the lows from the amp, and the dirty mids from the distorsion. The disto has to blend well with the guitars.
Sometimes you'll have the feeling that the two tracks do not blend very well, that there's a "gap" somewhere. Most of the time, I find that it's due to the lack of 500-1 khz in the amp sound, which really does the "link" between the distorsion and amp sound. Go back to the amp EQ.
At mix time, I'd use a compressor on the whole bass bus, hitting it hard, and then a Pultec style EQ to bring in/out more/less lows and more/less clarity (3 khz) if necessary, to make the bass sit in the mix.
After several months of research, I've found things that work pretty well :
First, getting a great sound out of the bass and amp is EXTREMELY important.
I had luck to achieve this Meshuggah kind of sound at tracking by doing this :
I splitted the signal outcoming from the bass :
1) First signal going into the amp. Ampeg amps and cabs are killer, they work for me. On the amp, move the EQ to get a great 90-120 Hz sound, thick and warm. Check the 250 Hz area, you don't won't too much of it to keep the clarity. I generally cut some 500 Hz here, but not too much. Then put a mic in front of the amp to capture this, MD421, D112... Route the mic into a good and punchy pre, and then into an EQ. Let's say Mindprint Dual Tube Channel channel 1. High pass at 35 Hz, low pass at 4 khz.
2) Second signal going into a DI for clean sound (something like REDDI, Avalon U5, depends on what you're after... but you need something that keeps your signal clean with thick but balanced bass/low meds and clarity in the 4-5 khz area).
3) Third signal going into a guitar distorsion pedal (POD or Sansamp GT2 for example), then into another DI (let's say API for punchy meds), then into a compressor (1176 works well) and into a parametric EQ (let's say Mindprint DTC channel 2). Play with the gain setting until it sounds good on the strings major hits. Turn down the lows and highs, boost the meds until they fit with the guitars tone if you already recorded them. Too much meds is too agressive, not sitting in the mix and fighting with the guitars a bit. Not enough meds is too dark, the bass sound will end into lacking of definition.
On the compressor, 4:1 or 6:1 ratio should work. -3 or -4 db of gain reduction is OK, with medium attack. Set the release time taking care of the playing : if the bassist isn't very consistant, long release works definitely, if the bassist has a great constant attack on the strings, shorten the release time should be a good thing.
On the EQ, high pass at 300-400 Hz, low pass at 3 Khz. Boost the **** out of 700 or 800 Hz, and 2,5 - 3 Khz, to get something very dirty and raw, than you can hear into the mix.
Listen to the disto and amp sound, they should blend well. The clean DI sound is there to bring back if something lacks at mix time, or to reamp if necessary.
The important thing is to get the lows from the amp, and the dirty mids from the distorsion. The disto has to blend well with the guitars.
Sometimes you'll have the feeling that the two tracks do not blend very well, that there's a "gap" somewhere. Most of the time, I find that it's due to the lack of 500-1 khz in the amp sound, which really does the "link" between the distorsion and amp sound. Go back to the amp EQ.
At mix time, I'd use a compressor on the whole bass bus, hitting it hard, and then a Pultec style EQ to bring in/out more/less lows and more/less clarity (3 khz) if necessary, to make the bass sit in the mix.
