Performance of site when loading 3000+ variables I test all modules (custom + contrib) in one drupal base itself which has resulted in lot of variables.
I was just curious what happens if live site had 3k variables ? 
Since all variables will be eventually global variables will it not require huge amount of PHP memory ? or is it not limited at all  ?
What is the alternate here ? cache_get with new cache table instead of variable_get every where
Yes, large variable tables are a problem.

Variables should only be used for small configuration flags and settings and not to store large structures for example.

But given a large amount of modules, dynamic variables like per-content type things you will sooner or later get into trouble.

No, there is no solution to this problem. The variables system will be replaced with the new configuration system from the CMI initiative for Drupal 8 which will hopefully be better at dealing with this.