I too am having a similar problem. I just purchased a Arduino Mega2560 R3 to see if it may be something my son could use for his robotics project since it has lots of program and SRAM space. I checked all the old and new troubleshooting forum info regarding hangs on UPLOADING. The DTR reset coupling cap is present and is indeed generating a reset. This issue exists with all example sketches so not my doing in code and not the "!!!" issue. Even doing manual resets just before the upload only work maybe 10% of the time. The only reliable way to get my Mega2560 to upload a sketch is to close the IDE, then reopen the IDE and sketch with the USB cable installed and immediately click upload. If I wait too long after opening the IDE or make edits after the first upload and try again, it hangs indefinately.
Still working on debugging the problem, but got this far after a few frustrating days. Haven't broke out the o-scope or LA yet. Running on WIN XP and the USB driver is correct. I started with Arduino 1.0 and just moved to 1.0.1 to see if the apparent bug was fixed, but still acts the same way. I have not read anywhere that this problem may have been fixed in a newer bootloader. When I get a chance I'll capture the verbose avr status info both when it works and fails.
Any thoughts from the long term experts would be welcome as it is a bit of a pain to exit out the IDE and restart every time I want to upload.