I now use a kinesis keyboard, which has two giant thumb keys for your left hand, I use those for control and meta. Before that I used control at caps-lock and meta using Ctrl+[, which worked well and pain-free for me for years.
Though I replaced my CAPSLOCK with CTRL and I mapped C-x C-m and C-c C-m to be equivalent to M-x. This dramatically reduce my usage of Alt.
What also helped is a tip borrowed from Steve Yegge [1] to bind C-x C-m to M-x (also C-c C-m, in case you miss the x). This avoids my most common use of Meta, allowing me to use the more comfortable Control (bound to Caps Lock).
[1] https://sites.google.com/site/steveyegge2/effective-emacs
[super] - [left meta] - [left control] - [space] - [right control] - [right meta]
Having control and meta right next to each other also makes C-M-* combinations easier to reach.