Okay, here is a quick workflow description for all of you that don't own Lightroom or Aftereffects.

You can use LRTimelapse as well with Bridge/ACR/Photoshop to get nice time lapse movies.

1. Open Adobe Bridge
   
2. Navigate to the Folder with your time lapse sequence
   
3. Select all images (Ctrl-A)
   
4. Open in Camera RAW (Ctrl-R)
   
5. Change development settings for the first image of the sequence
   
6. Select all images
   
7. Hit Synchronize, chose to sync everything
   
8. Edit the last image of the sequence if you want to make a transition
   
9. Hit Done.
   
10. Back in Bridge make sure the images have sequential suffixes
    

Now go to LRTimelapse. Open the Folder, make your transitions, deflicker (like I explained here)

Now open Photoshop

1. Chose File -> Open
   
2. Navigate to the folder with your image sequence
   
3. Select the first image
   
4. Check "image sequence"
   
5. Hit Open.
   
6. Chose a frame rate, i.e. 30 fps
   
7. You can check if the whole sequence was loaded under Window -> Workspace -> Motion. If only one image was loaded, the numbering of your files is not correct. I made best experiences with test-1000.jpg, test-1001.jpg and so on. (You can use the batch rename function in bridge to achieve this)
   
8. Now you can render the video via File->Export->Render Video.
   

Please make sure that you make every Image manipulation in Camera Raw, don't make any image manipulations in Photoshop!