The Amplitube Ampeg-SVX is nice, but a bit long in the tooth.  My go-to is the AD200 in the Amplitube Orange collection.  Sounds fantastic.

I also prefer keeping bass clean, or rather "unamped". I use different compression or EQ depending on the part. For a little saturation I've really liked Klanghelm SDRR. It has a few "styles", seems to add something I like and best of all it has a "mix" knob to set the balance between the dry signal and the processed one. Beware that the VST3 may misbehave in Sonar, depending on the chain. VST2 is fine though.

A multi band saturator is also great, for instance FabFilter Saturn - you can leave the lows untouched and dirty up the mids. Of course you can also do those things by cloning your bass track (optionally using LP MB as a crossover) but I personally prefer to keep it simple.

I use this:
http://www.uaudio.com/uad-plugins/ampeg-b15n.html
 
Unfortunately a bit expensive.
 

PLUS 1 on THambrecht and the UAD Ampeg amps.  Absolutely LOVE THEM.
 
 

I really like the Line 6 Bass POD.

Until recently I was using Amplitube GK and Fender bass amps and preferred them over Ampeg and Orange. TH3 is equally great. Now I find "Chuckebaby" way much more pleasant for my ears, in my case direct into audio interface (love my soundcard preamp), and add compression with Nomad BusDriver , an excellent $5 pluggin. If you prefer an amp coloration then cabinets IRs are much more important than amp choice, you may want to check Rosen Digital or Kazrog. 

Don't forget Audiffed GK Amplification Pro 2!! I have all the ones already mentioned and they all are great. If you are looking for the Gallien-Krueger flavor, you can't go wrong there. It was my goto bass amp sim for years and still fills the bill for that special bass tone that others don't fill.

This is an awesome thread. I just want to say thanks to everyone contributing with suggestions, ideas, an techniques.

I agree with Chuck Jones.  I stopped using bass amp sims a while ago.  The path I use to great sounding real bass is a great sounding, in tune bass plugged into a nice direct box ( I use the Neve RNDI but still love my old ART Tube Pac) into a good mic pre into my interface.
Once I've recorded and bounced my bass performance to a file, I make 2 clone audio tracks of the file.
I low pass the DI track at 600hz, insert a Waves CLA 1176 and use that purely for my clean bottom end sound.
On track 2 of the clone I'll high pass at 600hz and insert a Waves CLA bass plugin for punch and just boost a little top end on the eq. To achieve the amp in a room sound I'll send that track to the room reverb aux mixed about 15% giving it realistic depth.
On track 3 of the clone I'll high pass at 250hz and run Decapitator for harmonic distortion and grit.  Blending track 3 to taste with 1 and 2 gives a great bass sound.  
I'll then send all 3 tracks to a bus and insert a multiband compressor on it. On the bus EQ I'll boost 60hz about 3db and cut 100hz at 4db.  Also pull out 4db at 400.  Mud there.  Boost 2.5db at 5k.   Et viola!  Full, 3 dimensional bass sound without flattening it out with a amp sim.
 
Mark.
 

dlesaux
I use Overloud's Mark Studio. I think it's very flexible and sits well in the mix. Follow that with a preset in bReverb called Bass Room and you've got a real nice bass sound.

Markbass for me too, but I've never used a real bass amp to have a real world comparison.  am very happy with it, and surprised at the quality of tone I can can get from my squier JazzBass with flats.
 
89 euros if you have the TH3. I'm sure I picked it up for less with a sale, nearer 60Euros