Question: Most of my colleges have January 1 or January 15 deadlines. But, since I got my Regular Decision applications in early (just before Thanksgiving), will admission committees evaluate me based on only my grades through junior year, since my mid-term grades won't be out until long after I submitted my applications?
For Regular Decision, your colleges will definitely use your first quarter grades and almost always the first semester grades, too, unless they come out atypically late. It doesn't really matter when you submit your applications because, once colleges know the marking period has ended, they will want your senior grades before issuing a verdict. The Common Application has a Secondary School Mid-Year Report Form that says:
Please submit this form when midyear grades are available (end of first semester or second trimester). Attach applicant's official transcript, including courses in progress, a school profile, and transcript legend ...
Non-Common-App schools usually have their own version of this, too.
When students apply Early Decision or Early Action, then colleges MAY base their decision on junior grades only, although many will request first-quarter grades from the school counselor before deciding, if the counselor hasn't sent them. The same is true for "Rolling Admissions" colleges. When students apply early in the fall, Rolling Admissions colleges may make a decision right away without waiting for any senior grades, or admission officials may wait for first-quarter marks before deciding.
Students are sometimes misled into believing that junior grades are the ones that really "count," but, in fact, the start of senior year can be critical at admissions verdict time, and senior course selection is important, too. I've seen many students use their senior year as a chance to take all of those "fun" classes (silk-screening, psychology, ceramics ...) that they couldn't fit into their schedule earlier, when they were busy fulfilling requirements. And, while that sounds like a great idea to me, admission officials--especially at the more selective schools--will not view such choices in the same understanding light that I would.
So, hopefully, your senior grades and your senior courses will be up to snuff, since college folks will see--and use--them all when they seal your fate.