So, I play a real bass on all my tracks, and it's an important part of my writing and recording. I'm looking for a good bass amp sim. Great clean tones are a priority, but I also need flexibility depending on the song.

I have Sonar TH3, and the bass amps are fine, as far as they go.
Amplitube seem to have two offerings - Ampeg and Bass Bundle, and I don't really know the difference, or how good they are.
I have Waves GTR 3 and I struggle to get the bass amp sounds I want out of that. Maybe I should try harder, but amongst other things I yearn for a deep ultra clean tone.
I own S Gear and it's been rumoured that 3.0 will include a bass amp - judging by the fantastic quality of the guitar amps, I would have high hopes but it is currently an if but and maybe.
Others have mentioned Softube Bass Amp Room, but I read it was ilok. Not been down that road before, not sure what's involved.

I would love to hear your views on what you play your bass through.

Like Amplitube best, have the free versions 3 and 4 (hope they're still free by now).
Compared to other amp sims I find Amplitube just sounding more realistic.
Ignite amps have a free (donation optional iic) bass amp you could check out.

Guitar Rig 5 has a number of clean bass sounds.  I use it on all my songs these days.

I love the Amplitube Ampeg SVX.  
I used to use the "SVT" in Guitar Rig, and was quite happy with it until I tried Amplitube.
If I didn't want the Ampeg sound, i'd try the Bass Bundle, which simulates the Acoustic 360, Trace Elliot AH250, Sunn 1200S, and Fender Bassman.

Real Bass player over here also when I need a bass part for a tune I'm working on .
I will use what I have to use to get a decent performance into SONAR and then all bets are off
I have recorded w AmpliTube 4 and The Vandal full version ....
FWIW,  I don't think there is a bass amp sim that's gonna get me where I want to go using a Bass amp sim only ...
When recording my 4 string bass or my  8 string guitar , I have found that I much prefer to pretend that SPlat is a virtual collection of hardware gear that is there to use at my disposal ...
I treat my signal chain exactly as if I was using rack mount hardware as a pre amp combined w an amp sim ...
Very rarely will I use what comes with the stock amp sims them self's for my EQ or compression ...
I like to use per track effects going in before the amp sim and then combine that with the Pro Channel ...
 
all the best,
 
Kenny
 

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.

+1 to Amplitube Ampeg SVX - I use this on all of my real bass recordings

i own everything mentioned in this thread plus much more. now i only use bias amp pro or bias fx pro for my bass sim, it is leaps and bounds ahead of the rest imo, bass just sounds 'right' now, it's gorgeous. i wouldn't use anything else

I used to use every Bass amp sim you could think of until I went for a more realistic approach. (no not an amp)
Running the bass direct and using EQ, Compression and some saturation. there's your amp sim right there.
 
Any Sim will introduce characteristics but will also introduce noise as well.
I want the cleanest bass sound I can get. This mean a direct signal and applying FX. that's it.
I typically layer bass tracks though. some playing octaves, sometimes a distorted retro clav or pianos lows mixed in to create a bass sound as a whole. this takes practice and caution. If the layered tracks fall out of synch they become reversed polarity and cancel out the others signal thus sounding thin in areas.
 
Guitar amp Sims are another ballgame all together, more often than not your looking to reproduce an authentic tube sound. So a good amp sim is critical for those areas. Bass though, I have found its better left as clean as possible with only compression and EQ (and some saturation). Below is a list of FX and methods I use for hard rock by they still apply across the board:
 
*Do not use all at once. these are different methods to choose but I typically use 3 to 4 bass tracks in all.
1 main stringed bass guitar track and 2 or 3 alternatives mixed in a bit lower then the main bass track.
 
Recording:
- Bass direct in to a DI box
- Alesis 3630 Compressor 4:1 ratio using only light compression to round of spikes (go very light)
- New strings or boiled string for a snappy sound.
 
Plug ins:
- Softubes Grand Summit (EQ / Compressor)
- Softubes Saturation knob
- Cakewalks CA2A PC Module Compressor
- Cakewalks Percussion strip (EQ / Compressor)
 
Tracking:
- Double your tracks using a soft synth like SI Bass. use a higher frequency snappy setting.
- Double your tracks using a soft synth like Toontracks EZ Keys Grand piano (only the lower range of piano)
- Double your tracks using a soft synth like Toontracks EZ Keys Retro Clavinet (Distorted preset)
- Double your tracks using 2 more Bass tracks. Not played through the whole song but only on choruses, bridges ,exc..
  (play these parts on octaves).
 
This method can be heard here:
https://soundcloud.com/charlie-roy/seven

Just downloaded Amplitude and used the bass as aan amp effect on an existing midi bass track and it really added some punch to the song. Thanks for the tip!