Great thread and some great ideas!
1. I'll second Floatingbridge's mention of taking motifs and practicing them through changes. Because of the guitar's visual nature, I think motives is one of the few areas guitarists have an advantage over horn players, but yet it seems like horn players tend to use them more. I like to find some little lick on 2 adjacent strings and move that around a set of changes like All The Things or Solar, or a blues. Also this can be a good time to work in playing 3 on 4, or 5 on 3, etc.
2. Doing the above, but with 4ths, inverted 4ths, and triads.
3. This is an exercise I came up with for interval training. It's hard to explain, but bear with me: Pick two intervals. Play the first interval, then move the distance of the second interval, and play the first starting there. (Ok maybe just better to go to guitartabcreator.com)
For example, this would be M3 & P4:
E|-----5-----5--------------------------------------------------
B|--6-----6--------5-----5--------------------------------------
G|--------------5-----5--------4-----4--------------------------
D|--------------------------5-----5--------4-----4--------------
A|--------------------------------------5-----5--------4-----4--
E|--------------------------------------------------5-----5-----
This would be M6 & M3:
E|-----5-----5--------------------------------------
B|-----------------6-----6--------------------------
G|--5-----5--------------------6-----6--------------
D|--------------6-----6--------------------7-----7--
A|--------------------------7-----7-----------------
E|--------------------------------------8-----8-----
Go back up, practice downward intervals, etc. etc. etc.
4. I call it "Lick Inversion"....it's just taking a lick and starting on a different note, but it's amazing what you can discover melodically. Shaun Baxter calls it "Lick Rotation" and can explain it much better:
http://www.slideshare.net/edgararruda/part-3-the-lick-rotation-method
5. All Hammer ons and pulloffs:
E|--------------------------
B|--------------------------
G|--5--7--8--6--7--5--6--8--
D|--------------------------
A|--------------------------
E|--------------------------